diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/boot/ResourcesInitialization.scala b/engine/language-server/src/main/scala/org/enso/languageserver/boot/ResourcesInitialization.scala
index 1172e2f449..20a17b23e1 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/boot/ResourcesInitialization.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/boot/ResourcesInitialization.scala
@@ -9,10 +9,10 @@ import org.enso.languageserver.boot.resource.{
   TruffleContextInitialization
 }
 import org.enso.languageserver.data.DirectoriesConfig
-import org.enso.searcher.{FileVersionsRepo, SuggestionsRepo}
+import org.enso.searcher.sql.{SqlSuggestionsRepo, SqlVersionsRepo}
 import org.graalvm.polyglot.Context
 
-import scala.concurrent.{ExecutionContext, Future}
+import scala.concurrent.ExecutionContext
 
 /** Helper object for the initialization of the Language Server resources.
   * Creates the directories, initializes the databases, and the Truffle context.
@@ -31,13 +31,18 @@ object ResourcesInitialization {
   def apply(
     eventStream: EventStream,
     directoriesConfig: DirectoriesConfig,
-    suggestionsRepo: SuggestionsRepo[Future],
-    versionsRepo: FileVersionsRepo[Future],
+    suggestionsRepo: SqlSuggestionsRepo,
+    versionsRepo: SqlVersionsRepo,
     truffleContext: Context
   )(implicit ec: ExecutionContext): InitializationComponent = {
     val resources = Seq(
       new DirectoriesInitialization(directoriesConfig),
-      new RepoInitialization(eventStream, suggestionsRepo, versionsRepo),
+      new RepoInitialization(
+        directoriesConfig,
+        eventStream,
+        suggestionsRepo,
+        versionsRepo
+      ),
       new TruffleContextInitialization(eventStream, truffleContext)
     )
     new SequentialResourcesInitialization(resources)
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/boot/resource/RepoInitialization.scala b/engine/language-server/src/main/scala/org/enso/languageserver/boot/resource/RepoInitialization.scala
index 7d58126591..f35bd4a89f 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/boot/resource/RepoInitialization.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/boot/resource/RepoInitialization.scala
@@ -1,23 +1,31 @@
 package org.enso.languageserver.boot.resource
 
+import java.io.IOException
+import java.nio.file.{FileSystemException, Files, NoSuchFileException}
+
 import akka.event.EventStream
+import org.apache.commons.io.FileUtils
+import org.enso.languageserver.data.DirectoriesConfig
 import org.enso.languageserver.event.InitializedEvent
-import org.enso.searcher.{FileVersionsRepo, SuggestionsRepo}
+import org.enso.searcher.sql.{SqlDatabase, SqlSuggestionsRepo, SqlVersionsRepo}
 import org.slf4j.LoggerFactory
 
 import scala.concurrent.{ExecutionContext, Future}
+import scala.util.control.NonFatal
 import scala.util.{Failure, Success}
 
 /** Initialization of the Language Server repositories.
   *
+  * @param directoriesConfig configuration of language server directories
   * @param eventStream akka events stream
   * @param suggestionsRepo the suggestions repo
   * @param versionsRepo the versions repo
   */
 class RepoInitialization(
+  directoriesConfig: DirectoriesConfig,
   eventStream: EventStream,
-  suggestionsRepo: SuggestionsRepo[Future],
-  versionsRepo: FileVersionsRepo[Future]
+  suggestionsRepo: SqlSuggestionsRepo,
+  versionsRepo: SqlVersionsRepo
 )(implicit ec: ExecutionContext)
     extends InitializationComponent {
 
@@ -26,31 +34,131 @@ class RepoInitialization(
   /** @inheritdoc */
   override def init(): Future[InitializationComponent.Initialized.type] =
     for {
-      _ <- Future.sequence(Seq(suggestionsRepoInit, versionsRepoInit))
+      _ <- suggestionsRepoInit
+      _ <- versionsRepoInit
     } yield InitializationComponent.Initialized
 
   private def suggestionsRepoInit: Future[Unit] = {
-    val initAction = suggestionsRepo.init
+    val initAction =
+      for {
+        _ <- Future {
+          log.info(
+            s"Initializing suggestions repo " +
+            s"${directoriesConfig.suggestionsDatabaseFile}."
+          )
+        }
+        _ <- suggestionsRepo.init.recoverWith { case NonFatal(error) =>
+          recoverInitError(error, suggestionsRepo.db)
+        }
+        _ <- Future {
+          log.info(
+            s"Initialized Suggestions repo " +
+            s"${directoriesConfig.suggestionsDatabaseFile}."
+          )
+        }
+      } yield ()
     initAction.onComplete {
       case Success(()) =>
         eventStream.publish(InitializedEvent.SuggestionsRepoInitialized)
       case Failure(ex) =>
-        log.error("Failed to initialize SQL suggestions repo", ex)
+        log.error(
+          s"Failed to initialize SQL suggestions repo " +
+          s"${directoriesConfig.suggestionsDatabaseFile}. " +
+          s"${ex.getMessage}"
+        )
     }
-    log.info("Initialized Suggestions repo.")
     initAction
   }
 
   private def versionsRepoInit: Future[Unit] = {
-    val initAction = versionsRepo.init
+    val initAction =
+      for {
+        _ <- Future {
+          log.info(
+            s"Initializing versions repo " +
+            s"${directoriesConfig.suggestionsDatabaseFile}."
+          )
+        }
+        _ <- versionsRepo.init
+        _ <- Future {
+          log.info(
+            s"Initialized Versions repo " +
+            s"${directoriesConfig.suggestionsDatabaseFile}."
+          )
+        }
+      } yield ()
     initAction.onComplete {
       case Success(()) =>
         eventStream.publish(InitializedEvent.FileVersionsRepoInitialized)
       case Failure(ex) =>
-        log.error("Failed to initialize versions repo", ex)
+        log.error(
+          s"Failed to initialize SQL versions repo " +
+          s"${directoriesConfig.suggestionsDatabaseFile}. " +
+          s"${ex.getMessage}"
+        )
     }
-    log.info("Initialized Versions repo.")
     initAction
   }
 
+  private def recoverInitError(
+    error: Throwable,
+    db: SqlDatabase
+  ): Future[Unit] =
+    for {
+      _ <- Future {
+        log.warn(
+          s"Failed to initialize the suggestions database " +
+          s"${directoriesConfig.suggestionsDatabaseFile}. " +
+          s"${error.getMessage}"
+        )
+      }
+      _ <- Future(db.close())
+      _ <- clearDatabaseFile()
+      _ <- Future(db.open())
+      _ <- Future {
+        log.info("Retrying database initialization.")
+      }
+      _ <- suggestionsRepo.init
+    } yield ()
+
+  private def clearDatabaseFile(retries: Int = 0): Future[Unit] = {
+    Future {
+      log.info(s"Clear database file. Attempt #${retries + 1}.")
+      Files.delete(directoriesConfig.suggestionsDatabaseFile.toPath)
+    }.recoverWith {
+      case _: NoSuchFileException =>
+        log.warn(
+          s"Failed to delete the database file. Attempt #${retries + 1}. " +
+          s"File does not exist " +
+          s"${directoriesConfig.suggestionsDatabaseFile}"
+        )
+        Future.successful(())
+      case error: FileSystemException =>
+        log.error(
+          s"Failed to delete the database file. Attempt #${retries + 1}." +
+          s"The file will be removed during the shutdown. ${error.getMessage}."
+        )
+        sys.addShutdownHook(
+          FileUtils.deleteQuietly(directoriesConfig.suggestionsDatabaseFile)
+        )
+        Future.failed(error)
+      case error: IOException =>
+        log.error(
+          s"Failed to delete the database file. Attempt #${retries + 1}. " +
+          s"${error.getMessage}"
+        )
+        if (retries < RepoInitialization.MaxRetries) {
+          Thread.sleep(1000)
+          clearDatabaseFile(retries + 1)
+        } else {
+          Future.failed(error)
+        }
+    }
+  }
+
+}
+
+object RepoInitialization {
+
+  val MaxRetries = 3
 }
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala b/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
index 705bd0359f..88cd29d378 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/search/SuggestionsHandler.scala
@@ -402,6 +402,7 @@ final class SuggestionsHandler(
           }
           .pipeTo(self)
         context.become(verifying(name, graph))
+        unstashAll()
     }
   }
 
diff --git a/engine/language-server/src/main/scala/org/enso/languageserver/text/BufferRegistry.scala b/engine/language-server/src/main/scala/org/enso/languageserver/text/BufferRegistry.scala
index 429715b540..fd202e932a 100644
--- a/engine/language-server/src/main/scala/org/enso/languageserver/text/BufferRegistry.scala
+++ b/engine/language-server/src/main/scala/org/enso/languageserver/text/BufferRegistry.scala
@@ -1,6 +1,6 @@
 package org.enso.languageserver.text
 
-import akka.actor.{Actor, ActorLogging, ActorRef, Props, Terminated}
+import akka.actor.{Actor, ActorLogging, ActorRef, Props, Stash, Terminated}
 import org.enso.languageserver.capability.CapabilityProtocol.{
   AcquireCapability,
   CapabilityAcquisitionBadRequest,
@@ -8,6 +8,7 @@ import org.enso.languageserver.capability.CapabilityProtocol.{
   ReleaseCapability
 }
 import org.enso.languageserver.data.{CanEdit, CapabilityRegistration}
+import org.enso.languageserver.event.InitializedEvent
 import org.enso.languageserver.filemanager.Path
 import org.enso.languageserver.monitoring.MonitoringProtocol.{Ping, Pong}
 import org.enso.languageserver.util.UnhandledLogging
@@ -66,10 +67,27 @@ class BufferRegistry(
 )(implicit
   versionCalculator: ContentBasedVersioning
 ) extends Actor
+    with Stash
     with ActorLogging
     with UnhandledLogging {
 
-  override def receive: Receive = running(Map.empty)
+  override def preStart(): Unit = {
+    log.info("Starting initialization.")
+    context.system.eventStream
+      .subscribe(self, InitializedEvent.FileVersionsRepoInitialized.getClass)
+  }
+
+  override def receive: Receive = initializing
+
+  private def initializing: Receive = {
+    case InitializedEvent.FileVersionsRepoInitialized =>
+      log.info("Initiaized.")
+      context.become(running(Map.empty))
+      unstashAll()
+
+    case _ =>
+      stash()
+  }
 
   private def running(registry: Map[Path, ActorRef]): Receive = {
     case Ping =>
diff --git a/engine/language-server/src/test/scala/org/enso/languageserver/boot/resource/RepoInitializationSpec.scala b/engine/language-server/src/test/scala/org/enso/languageserver/boot/resource/RepoInitializationSpec.scala
new file mode 100644
index 0000000000..cbd79bb7ca
--- /dev/null
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/boot/resource/RepoInitializationSpec.scala
@@ -0,0 +1,254 @@
+package org.enso.languageserver.boot.resource
+
+import java.io.File
+import java.nio.file.{Files, StandardOpenOption}
+import java.util.UUID
+
+import akka.actor.ActorSystem
+import akka.testkit._
+import org.apache.commons.io.FileUtils
+import org.enso.languageserver.data._
+import org.enso.languageserver.event.InitializedEvent
+import org.enso.searcher.sql.{
+  SchemaVersion,
+  SqlDatabase,
+  SqlSuggestionsRepo,
+  SqlVersionsRepo
+}
+import org.enso.testkit.FlakySpec
+import org.scalatest.BeforeAndAfterAll
+import org.scalatest.matchers.should.Matchers
+import org.scalatest.wordspec.AnyWordSpecLike
+import org.sqlite.SQLiteException
+
+import scala.concurrent.Await
+import scala.concurrent.duration._
+
+class RepoInitializationSpec
+    extends TestKit(ActorSystem("TestSystem"))
+    with ImplicitSender
+    with AnyWordSpecLike
+    with Matchers
+    with BeforeAndAfterAll
+    with FlakySpec {
+
+  import system.dispatcher
+
+  val Timeout: FiniteDuration = 10.seconds.dilated
+
+  override def afterAll(): Unit = {
+    TestKit.shutdownActorSystem(system)
+  }
+
+  "RepoInitialization" should {
+
+    "initialize repositories" in withDb {
+      (config, suggestionsRepo, versionsRepo) =>
+        system.eventStream.subscribe(self, classOf[InitializedEvent])
+
+        val component =
+          new RepoInitialization(
+            config.directories,
+            system.eventStream,
+            suggestionsRepo,
+            versionsRepo
+          )
+
+        val action =
+          for {
+            _             <- component.init()
+            schemaVersion <- suggestionsRepo.getSchemaVersion
+          } yield schemaVersion
+
+        val version = Await.result(action, Timeout)
+        version shouldEqual SchemaVersion.CurrentVersion
+
+        expectMsgAllOf(
+          InitializedEvent.SuggestionsRepoInitialized,
+          InitializedEvent.FileVersionsRepoInitialized
+        )
+    }
+
+    "recreate suggestion database when schema version is incorrect" in withDb {
+      (config, suggestionsRepo, versionsRepo) =>
+        system.eventStream.subscribe(self, classOf[InitializedEvent])
+
+        val testSchemaVersion = Long.MaxValue
+        val component =
+          new RepoInitialization(
+            config.directories,
+            system.eventStream,
+            suggestionsRepo,
+            versionsRepo
+          )
+
+        val action =
+          for {
+            _       <- suggestionsRepo.init
+            _       <- suggestionsRepo.setSchemaVersion(testSchemaVersion)
+            _       <- component.init()
+            version <- suggestionsRepo.getSchemaVersion
+          } yield version
+
+        val version = Await.result(action, Timeout)
+        version shouldEqual SchemaVersion.CurrentVersion
+
+        expectMsgAllOf(
+          InitializedEvent.SuggestionsRepoInitialized,
+          InitializedEvent.FileVersionsRepoInitialized
+        )
+    }
+
+    "recreate suggestion database when schema version is empty" in withDb {
+      (config, suggestionsRepo, versionsRepo) =>
+        system.eventStream.subscribe(self, classOf[InitializedEvent])
+
+        val component =
+          new RepoInitialization(
+            config.directories,
+            system.eventStream,
+            suggestionsRepo,
+            versionsRepo
+          )
+
+        // initialize
+        val init =
+          for {
+            _       <- component.init()
+            version <- suggestionsRepo.getSchemaVersion
+          } yield version
+
+        val version1 = Await.result(init, Timeout)
+        version1 shouldEqual SchemaVersion.CurrentVersion
+        expectMsgAllOf(
+          InitializedEvent.SuggestionsRepoInitialized,
+          InitializedEvent.FileVersionsRepoInitialized
+        )
+
+        // remove schema and re-initialize
+        val action =
+          for {
+            _       <- suggestionsRepo.clearSchemaVersion
+            _       <- component.init()
+            version <- suggestionsRepo.getSchemaVersion
+          } yield version
+
+        val version2 = Await.result(action, Timeout)
+        version2 shouldEqual SchemaVersion.CurrentVersion
+        expectMsgAllOf(
+          InitializedEvent.SuggestionsRepoInitialized,
+          InitializedEvent.FileVersionsRepoInitialized
+        )
+    }
+
+    "recreate corrupted suggestion database file" taggedAs Flaky in withConfig {
+      config =>
+        // initialize
+        withRepos(config) { (suggestionsRepo, versionsRepo) =>
+          val component =
+            new RepoInitialization(
+              config.directories,
+              system.eventStream,
+              suggestionsRepo,
+              versionsRepo
+            )
+
+          val init =
+            for {
+              _       <- component.init()
+              version <- suggestionsRepo.getSchemaVersion
+            } yield version
+
+          val version1 = Await.result(init, Timeout)
+          version1 shouldEqual SchemaVersion.CurrentVersion
+        }
+
+        // corrupt
+        val bytes: Array[Byte] = Array(1, 2, 3)
+        Files.delete(config.directories.suggestionsDatabaseFile.toPath)
+        Files.write(
+          config.directories.suggestionsDatabaseFile.toPath,
+          bytes,
+          StandardOpenOption.CREATE
+        )
+        withRepos(config) { (suggestionsRepo, _) =>
+          an[SQLiteException] should be thrownBy Await.result(
+            suggestionsRepo.getSchemaVersion,
+            Timeout
+          )
+        }
+
+        // re-initialize
+        withRepos(config) { (suggestionsRepo, versionsRepo) =>
+          val component =
+            new RepoInitialization(
+              config.directories,
+              system.eventStream,
+              suggestionsRepo,
+              versionsRepo
+            )
+
+          val action =
+            for {
+              _       <- component.init()
+              version <- suggestionsRepo.getSchemaVersion
+            } yield version
+
+          val version2 = Await.result(action, Timeout)
+          version2 shouldEqual SchemaVersion.CurrentVersion
+          expectMsgAllOf(
+            InitializedEvent.SuggestionsRepoInitialized,
+            InitializedEvent.FileVersionsRepoInitialized
+          )
+        }
+    }
+
+  }
+
+  def newConfig(root: File): Config = {
+    Config(
+      Map(UUID.randomUUID() -> root),
+      FileManagerConfig(timeout = 3.seconds.dilated),
+      PathWatcherConfig(),
+      ExecutionContextConfig(requestTimeout = 3.seconds.dilated),
+      DirectoriesConfig.initialize(root)
+    )
+  }
+
+  def withConfig(test: Config => Any): Unit = {
+    val testContentRoot = Files.createTempDirectory(null).toRealPath()
+    sys.addShutdownHook(FileUtils.deleteQuietly(testContentRoot.toFile))
+    val config = newConfig(testContentRoot.toFile)
+
+    test(config)
+  }
+
+  def withRepos(
+    config: Config
+  )(test: (SqlSuggestionsRepo, SqlVersionsRepo) => Any): Unit = {
+    val sqlDatabase = SqlDatabase(
+      config.directories.suggestionsDatabaseFile.toString
+    )
+    val suggestionsRepo = new SqlSuggestionsRepo(sqlDatabase)
+    val versionsRepo    = new SqlVersionsRepo(sqlDatabase)
+
+    try test(suggestionsRepo, versionsRepo)
+    finally {
+      sqlDatabase.close()
+    }
+  }
+
+  def withDb(
+    test: (
+      Config,
+      SqlSuggestionsRepo,
+      SqlVersionsRepo
+    ) => Any
+  ): Unit = {
+    withConfig { config =>
+      withRepos(config) { (suggestionsRepo, versionsRepo) =>
+        test(config, suggestionsRepo, versionsRepo)
+      }
+    }
+  }
+}
diff --git a/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala b/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala
index 56dac6f52c..76852304e5 100644
--- a/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/runtime/ContextEventsListenerSpec.scala
@@ -408,12 +408,16 @@ class ContextEventsListenerSpec
         updatesSendRate
       )
     )
-    repo.init.onComplete {
+    val repoInit = repo.init
+    repoInit.onComplete {
       case Success(()) =>
         system.eventStream.publish(InitializedEvent.SuggestionsRepoInitialized)
       case Failure(ex) =>
-        system.log.error(ex, "Failed to initialize Suggestions repo")
+        system.log.error(
+          s"ContextEventsListenerSpec failed to initialize Suggestions repo. $ex"
+        )
     }
+    Await.ready(repoInit, Timeout)
 
     try test(clientId, contextId, repo, router, listener)
     finally {
diff --git a/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/BaseServerTest.scala b/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/BaseServerTest.scala
index ab6d08081f..6b338f0161 100644
--- a/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/BaseServerTest.scala
+++ b/engine/language-server/src/test/scala/org/enso/languageserver/websocket/json/BaseServerTest.scala
@@ -105,7 +105,12 @@ class BaseServerTest extends JsonRpcServerTestKit {
 
   val initializationComponent = SequentialResourcesInitialization(
     new DirectoriesInitialization(config.directories),
-    new RepoInitialization(system.eventStream, suggestionsRepo, versionsRepo)
+    new RepoInitialization(
+      config.directories,
+      system.eventStream,
+      suggestionsRepo,
+      versionsRepo
+    )
   )
 
   override def clientControllerFactory: ClientControllerFactory = {
diff --git a/lib/scala/searcher/src/main/resources/reference.conf b/lib/scala/searcher/src/main/resources/reference.conf
index f2520be795..0714cd12f1 100644
--- a/lib/scala/searcher/src/main/resources/reference.conf
+++ b/lib/scala/searcher/src/main/resources/reference.conf
@@ -3,7 +3,7 @@ searcher {
     url = "jdbc:sqlite::memory:"
     driver = "org.sqlite.JDBC"
     connectionPool = disabled
-    properties.journal_mode = "wal"
+    properties.journal_mode = "memory"
     properties.locking_mode = "EXCLUSIVE"
     numThreads = 1
   }
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/Database.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/Database.scala
index 71ce876d35..8fdf768c79 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/Database.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/Database.scala
@@ -13,8 +13,8 @@ trait Database[F[_], G[_]] {
     */
   def run[A](query: F[A]): G[A]
 
-  /** Run the database query in one transaction */
-  def transaction[A](query: F[A]): G[A]
+  /** Open the database. */
+  def open(): Unit
 
   /** Close the database. */
   def close(): Unit
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/InvalidSchemaVersion.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/InvalidSchemaVersion.scala
new file mode 100644
index 0000000000..e43c8f0d5d
--- /dev/null
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/InvalidSchemaVersion.scala
@@ -0,0 +1,11 @@
+package org.enso.searcher.sql
+
+/** An error indicating that the database has invalid schema version.
+  *
+  * @param version the database schema version.
+  */
+class InvalidSchemaVersion(val version: Long)
+    extends RuntimeException(
+      s"Database schema version '$version' is different from the application " +
+      s"schema version '${SchemaVersion.CurrentVersion}'."
+    )
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlDatabase.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlDatabase.scala
index f9dc4d4814..af3cde794d 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlDatabase.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlDatabase.scala
@@ -5,7 +5,6 @@ import org.enso.searcher.Database
 import org.enso.searcher.sqlite.LockingMode
 import slick.dbio.DBIO
 import slick.jdbc.SQLiteProfile
-import slick.jdbc.SQLiteProfile.api._
 
 import scala.concurrent.Future
 
@@ -16,20 +15,26 @@ import scala.concurrent.Future
 final class SqlDatabase(config: Option[Config] = None)
     extends Database[DBIO, Future] {
 
-  val db = SQLiteProfile.backend.Database
-    .forConfig(SqlDatabase.configPath, config.orNull)
+  private var db: SQLiteProfile.backend.Database = _
+
+  open()
 
   /** @inheritdoc */
   override def run[A](query: DBIO[A]): Future[A] =
     db.run(query)
 
   /** @inheritdoc */
-  override def transaction[A](query: DBIO[A]): Future[A] =
-    db.run(query.transactionally)
+  override def open(): Unit =
+    this.synchronized {
+      db = SQLiteProfile.backend.Database
+        .forConfig(SqlDatabase.configPath, config.orNull)
+    }
 
   /** @inheritdoc */
   override def close(): Unit =
-    db.close()
+    this.synchronized {
+      db.close()
+    }
 }
 
 object SqlDatabase {
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
index b8de4e1a2a..e7472451bd 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlSuggestionsRepo.scala
@@ -1,5 +1,8 @@
 package org.enso.searcher.sql
 
+import java.io.File
+import java.util.UUID
+
 import org.enso.polyglot.Suggestion
 import org.enso.polyglot.data.Tree
 import org.enso.polyglot.runtime.Runtime.Api.{
@@ -10,18 +13,18 @@ import org.enso.polyglot.runtime.Runtime.Api.{
 }
 import org.enso.searcher.data.QueryResult
 import org.enso.searcher.{SuggestionEntry, SuggestionsRepo}
-import slick.jdbc.SQLiteProfile
 import slick.jdbc.SQLiteProfile.api._
+import slick.jdbc.meta.MTable
+import slick.relational.RelationalProfile
 
-import java.io.File
-import java.util.UUID
 import scala.collection.immutable.HashMap
 import scala.concurrent.{ExecutionContext, Future}
 import scala.util.{Failure, Success}
 
 /** The object for accessing the suggestions database. */
-final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
-    extends SuggestionsRepo[Future] {
+final class SqlSuggestionsRepo(val db: SqlDatabase)(implicit
+  ec: ExecutionContext
+) extends SuggestionsRepo[Future] {
 
   /** The query returning the arguments joined with the corresponding
     * suggestions.
@@ -155,6 +158,25 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
   def close(): Unit =
     db.close()
 
+  /** Get the database schema version.
+    *
+    * @return the schema version of the database
+    */
+  def getSchemaVersion: Future[Long] =
+    db.run(currentSchemaVersionQuery)
+
+  /** Set the database schema version.
+    *
+    * @param version the database schema version
+    * @return the schema version of the database
+    */
+  def setSchemaVersion(version: Long): Future[Long] =
+    db.run(setSchemaVersionQuery(version))
+
+  /** Remove the database schema version. */
+  def clearSchemaVersion: Future[Unit] =
+    db.run(clearSchemaVersionQuery)
+
   /** Insert suggestions in a batch.
     *
     * @param suggestions the list of suggestions to insert
@@ -165,12 +187,33 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
 
   /** The query to initialize the repo. */
   private def initQuery: DBIO[Unit] = {
-    // Initialize schema suppressing errors. Workaround for slick/slick#1999.
-    def initSchema(schema: SQLiteProfile.SchemaDescription) =
-      schema.createIfNotExists.asTry >> DBIO.successful(())
-    val schemas =
-      Seq(Suggestions.schema, Arguments.schema, SuggestionsVersions.schema)
-    DBIO.sequence(schemas.map(initSchema)) >> DBIO.successful(())
+    type RelationalTable[A] = RelationalProfile#Table[A]
+    def checkVersion(version: Long) =
+      if (version == SchemaVersion.CurrentVersion) {
+        DBIO.successful(())
+      } else {
+        DBIO.failed(new InvalidSchemaVersion(version))
+      }
+    def createSchema(table: TableQuery[RelationalTable[_]]) =
+      for {
+        tables <- MTable.getTables(table.shaped.value.tableName)
+        _      <- if (tables.isEmpty) table.schema.create else DBIO.successful(())
+      } yield ()
+
+    val tables: Seq[TableQuery[RelationalTable[_]]] =
+      Seq(Suggestions, Arguments, SuggestionsVersions, SchemaVersion)
+        .asInstanceOf[Seq[TableQuery[RelationalTable[_]]]]
+    val initSchemas =
+      for {
+        _       <- DBIO.sequence(tables.map(createSchema))
+        version <- initSchemaVersionQuery
+      } yield version
+
+    for {
+      versionAttempt <- currentSchemaVersionQuery.asTry
+      version        <- versionAttempt.fold(_ => initSchemas, DBIO.successful)
+      _              <- checkVersion(version)
+    } yield ()
   }
 
   /** The query to clean the repo. */
@@ -713,6 +756,37 @@ final class SqlSuggestionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
     incrementQuery
   }
 
+  /** The query to get current version of the repo. */
+  private def currentSchemaVersionQuery: DBIO[Long] = {
+    for {
+      versionOpt <- SchemaVersion.result.headOption
+    } yield versionOpt.flatMap(_.id).getOrElse(0L)
+  }
+
+  /** The query to initialize the [[SchemaVersion]] table. */
+  private def initSchemaVersionQuery: DBIO[Long] = {
+    setSchemaVersionQuery(SchemaVersion.CurrentVersion)
+  }
+
+  /** The query setting the schema version.
+    *
+    * @param version the schema version.
+    * @return the current value of the schema version
+    */
+  private def setSchemaVersionQuery(version: Long): DBIO[Long] = {
+    val query = for {
+      _ <- SchemaVersion.delete
+      _ <- SchemaVersion += SchemaVersionRow(Some(version))
+    } yield version
+    query
+  }
+
+  /** The query to delete the schema version. */
+  private def clearSchemaVersionQuery: DBIO[Unit] =
+    for {
+      _ <- SchemaVersion.delete
+    } yield ()
+
   /** The query to insert suggestions in a batch.
     *
     * @param suggestions the list of suggestions to insert
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
index c1c7afbe65..c847d3da7c 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/SqlVersionsRepo.scala
@@ -5,6 +5,7 @@ import java.util
 
 import org.enso.searcher.FileVersionsRepo
 import slick.jdbc.SQLiteProfile.api._
+import slick.jdbc.meta.MTable
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -50,8 +51,11 @@ final class SqlVersionsRepo(db: SqlDatabase)(implicit ec: ExecutionContext)
 
   /** The query to initialize the repo. */
   private def initQuery: DBIO[Unit] = {
-    // Initialize schema suppressing errors. Workaround for slick/slick#1999.
-    FileVersions.schema.createIfNotExists.asTry >> DBIO.successful(())
+    val table = FileVersions
+    for {
+      tables <- MTable.getTables(table.shaped.value.tableName)
+      _      <- if (tables.isEmpty) table.schema.create else DBIO.successful(())
+    } yield ()
   }
 
   /** The query to clean the repo. */
diff --git a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/Tables.scala b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/Tables.scala
index 8318a0ee0e..ccd5f6ba6d 100644
--- a/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/Tables.scala
+++ b/lib/scala/searcher/src/main/scala/org/enso/searcher/sql/Tables.scala
@@ -65,6 +65,12 @@ case class SuggestionRow(
   */
 case class SuggestionsVersionRow(id: Option[Long])
 
+/** A row in the schema_version table.
+  *
+  * @param id the row id
+  */
+case class SchemaVersionRow(id: Option[Long])
+
 /** A row in the file_versions table
   *
   * @param path the file path
@@ -206,16 +212,6 @@ final class SuggestionsTable(tag: Tag)
     )
 }
 
-/** The schema of the suggestions_version table. */
-@nowarn("msg=multiarg infix syntax")
-final class SuggestionsVersionTable(tag: Tag)
-    extends Table[SuggestionsVersionRow](tag, "suggestions_version") {
-
-  def id = column[Long]("id", O.PrimaryKey, O.AutoInc)
-
-  def * = id.? <> (SuggestionsVersionRow.apply, SuggestionsVersionRow.unapply)
-}
-
 /** The schema of the file_versions table. */
 @nowarn("msg=multiarg infix syntax")
 final class FileVersionsTable(tag: Tag)
@@ -227,10 +223,36 @@ final class FileVersionsTable(tag: Tag)
   def * = (path, digest) <> (FileVersionRow.tupled, FileVersionRow.unapply)
 }
 
+/** The schema of the suggestions_version table. */
+@nowarn("msg=multiarg infix syntax")
+final class SuggestionsVersionTable(tag: Tag)
+    extends Table[SuggestionsVersionRow](tag, "suggestions_version") {
+
+  def id = column[Long]("id", O.PrimaryKey, O.AutoInc)
+
+  def * = id.? <> (SuggestionsVersionRow.apply, SuggestionsVersionRow.unapply)
+}
+
+/** The schema of the schema_version table. */
+@nowarn("msg=multiarg infix syntax")
+final class SchemaVersionTable(tag: Tag)
+    extends Table[SchemaVersionRow](tag, "schema_version") {
+
+  def id = column[Long]("id", O.PrimaryKey)
+
+  def * = id.? <> (SchemaVersionRow.apply, SchemaVersionRow.unapply)
+}
+
 object Arguments extends TableQuery(new ArgumentsTable(_))
 
 object Suggestions extends TableQuery(new SuggestionsTable(_))
 
+object FileVersions extends TableQuery(new FileVersionsTable(_))
+
 object SuggestionsVersions extends TableQuery(new SuggestionsVersionTable(_))
 
-object FileVersions extends TableQuery(new FileVersionsTable(_))
+object SchemaVersion extends TableQuery(new SchemaVersionTable(_)) {
+
+  /** The current schema version. */
+  val CurrentVersion: Long = 1
+}
diff --git a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
index 654bfb0247..6d6a1c7652 100644
--- a/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
+++ b/lib/scala/searcher/src/test/scala/org/enso/searcher/sql/SuggestionsRepoTest.scala
@@ -45,6 +45,19 @@ class SuggestionsRepoTest extends AnyWordSpec with Matchers with RetrySpec {
       Await.result(repo.init, Timeout)
     }
 
+    "check the schema version when init" taggedAs Retry in withRepo { repo =>
+      val wrongSchemaVersion = Long.MinValue
+      val action =
+        for {
+          version <- repo.setSchemaVersion(wrongSchemaVersion)
+          _       <- repo.init
+        } yield version
+
+      val thrown =
+        the[InvalidSchemaVersion] thrownBy Await.result(action, Timeout)
+      thrown.version shouldEqual wrongSchemaVersion
+    }
+
     "get all suggestions" taggedAs Retry in withRepo { repo =>
       val action =
         for {