diff --git a/engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/instrument/RuntimeManagementCleanupTest.java b/engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/instrument/RuntimeManagementCleanupTest.java
new file mode 100644
index 0000000000..25e31b1155
--- /dev/null
+++ b/engine/runtime-integration-tests/src/test/java/org/enso/interpreter/test/instrument/RuntimeManagementCleanupTest.java
@@ -0,0 +1,35 @@
+package org.enso.interpreter.test.instrument;
+
+import static org.junit.Assert.fail;
+
+import java.io.OutputStream;
+import java.io.PrintStream;
+import org.junit.Test;
+
+public final class RuntimeManagementCleanupTest {
+
+  @Test
+  public void cleanUp() throws InterruptedException {
+    var cnt = 0;
+    for (var i = 1; i < 100; i++) {
+      cnt = 0;
+      var err = i % 10 == 0 ? System.err : new PrintStream(OutputStream.nullOutputStream());
+      for (var threadStack : Thread.getAllStackTraces().entrySet()) {
+        if (threadStack.getKey().getName().startsWith("Thread-")) {
+          err.println(threadStack.getKey().getName());
+          for (var frame : threadStack.getValue()) {
+            err.println("  " + frame);
+          }
+          cnt++;
+        }
+      }
+      err.println("Found " + cnt + " suspicious threads");
+      if (cnt == 0) {
+        return;
+      }
+      System.gc();
+      Thread.sleep(100);
+    }
+    fail("There are still " + cnt + " suspicious threads");
+  }
+}
diff --git a/engine/runtime/src/main/java/org/enso/interpreter/runtime/ResourceManager.java b/engine/runtime/src/main/java/org/enso/interpreter/runtime/ResourceManager.java
index 5a9bbaad62..b8295c6b94 100644
--- a/engine/runtime/src/main/java/org/enso/interpreter/runtime/ResourceManager.java
+++ b/engine/runtime/src/main/java/org/enso/interpreter/runtime/ResourceManager.java
@@ -7,23 +7,49 @@ import java.lang.ref.PhantomReference;
 import java.lang.ref.Reference;
 import java.lang.ref.ReferenceQueue;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.concurrent.ConcurrentMap;
 import java.util.concurrent.Future;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
+import java.util.function.Function;
 import org.enso.interpreter.runtime.data.ManagedResource;
 
 /** Allows the context to attach garbage collection hooks on the removal of certain objects. */
 public final class ResourceManager {
-  private final EnsoContext context;
-  private volatile boolean isClosed = false;
-  private volatile Thread workerThread;
-  private final ProcessItems worker = new ProcessItems();
+  /** Amount of milliseconds to wait for another resource when none is pending. */
+  private static final long KEEP_ALIVE = 1000;
+
+  /** Queue with resources eligible for finalization */
   private final ReferenceQueue<ManagedResource> referenceQueue = new ReferenceQueue<>();
-  private final ConcurrentMap<PhantomReference<ManagedResource>, Item> items =
-      new ConcurrentHashMap<>();
+
+  /**
+   * All the items that were issued, but haven't yet arrived at {@link #referenceQueue} for
+   * finalization.
+   *
+   * <p>@GuardedBy("this")
+   */
+  private final List<Item> pendingItems = new ArrayList<>();
+
+  private final EnsoContext context;
+
+  /**
+   * Indicates this manager is closed. If assigned to {@code processor} field, this manager is
+   * considered closed.
+   */
+  private final ProcessItems CLOSED = new ProcessItems(null);
+
+  /**
+   * The current processor (with own worker {@link Thread}) that is supposed to await {@link
+   * #removeNextQueuedItem(ProcessItems)} and process them by properly invoking their finalizers
+   * using a safepoint action.
+   *
+   * <p>If this field is set to {@link #CLOSED}, then this resource manager is considered to be
+   * closed.
+   *
+   * <p>@GuardedBy("this")
+   */
+  private ProcessItems processor;
 
   /**
    * Creates a new instance of Resource Manager.
@@ -60,11 +86,6 @@ public final class ResourceManager {
     }
   }
 
-  @CompilerDirectives.TruffleBoundary
-  private Item removeFromItems(PhantomReference<ManagedResource> it) {
-    return items.remove(it);
-  }
-
   /**
    * Manually and unconditionally finalizes the resource. Ignores the parking mechanism, assuming
    * the user now has full control over the resource.
@@ -100,20 +121,15 @@ public final class ResourceManager {
    * @return a wrapper object, containing the resource and serving as a reachability probe
    */
   @CompilerDirectives.TruffleBoundary
-  public ManagedResource register(Object object, Object function) {
-    if (isClosed) {
+  public synchronized ManagedResource register(Object object, Object function) {
+    if (CLOSED == processor) {
       throw EnsoContext.get(null)
           .raiseAssertionPanic(
               null, "Can't register new resources after resource manager is closed.", null);
     }
-    if (workerThread == null || !workerThread.isAlive()) {
-      worker.setKilled(false);
-      workerThread = context.createThread(true, worker);
-      workerThread.start();
-    }
     var resource = new ManagedResource(object, r -> new Item(r, object, function, referenceQueue));
     var ref = (Item) resource.getPhantomReference();
-    items.put(ref, ref);
+    addPendingItem(ref);
     return resource;
   }
 
@@ -125,25 +141,92 @@ public final class ResourceManager {
    * will be run in it.
    */
   public void shutdown() {
-    isClosed = true;
-    worker.setKilled(true);
-    if (workerThread != null) {
-      while (true) {
-        try {
-          workerThread.interrupt();
-          workerThread.join();
-          break;
-        } catch (InterruptedException ignored) {
-        }
+    Item[] toFinalize;
+    ProcessItems lastProcessor;
+    synchronized (this) {
+      if (processor == CLOSED) {
+        // already shut(-ting) down
+        return;
       }
+      toFinalize = pendingItems.toArray(Item[]::new);
+      lastProcessor = processor;
+      processor = CLOSED;
     }
-    for (PhantomReference<ManagedResource> key : items.keySet()) {
-      Item it = removeFromItems(key);
-      if (it != null) {
+    if (lastProcessor != null) {
+      for (var it : lastProcessor.awaitShutdown()) {
         // Finalize unconditionally – all other threads are dead by now.
         it.finalizeNow(context);
       }
     }
+    for (var it : toFinalize) {
+      // Finalize unconditionally – these items weren't picked by any thread.
+      it.finalizeNow(context);
+    }
+  }
+
+  /**
+   * Adds pending item into the existing processor. If there is no processor, it allocates new and
+   * starts its processing thread.
+   */
+  @CompilerDirectives.TruffleBoundary
+  private synchronized void addPendingItem(Item item) {
+    if (processor == null) {
+      processor = new ProcessItems(r -> context.createThread(true, r));
+    }
+    pendingItems.add(item);
+  }
+
+  @CompilerDirectives.TruffleBoundary
+  private synchronized void removeFromItems(PhantomReference<ManagedResource> it) {
+    if (it instanceof Item item) {
+      pendingItems.remove(item);
+      if (pendingItems.isEmpty() && processor != null) {
+        processor.awake();
+      }
+    }
+  }
+
+  /**
+   * Awaits next item in the queue, if any.
+   *
+   * @param p the processor that queries
+   * @return item from queue or {@code null} if {@code p} processor may be eligible for a shutdown
+   */
+  @CompilerDirectives.TruffleBoundary
+  private Reference<? extends ManagedResource> removeNextQueuedItem(ProcessItems p) {
+    boolean empty;
+    synchronized (this) {
+      if (processor != p) {
+        return null;
+      }
+      assert Thread.currentThread() == p.workerThread;
+      assert p.isActive();
+      empty = pendingItems.isEmpty();
+    }
+    try {
+      if (empty) {
+        return referenceQueue.remove(KEEP_ALIVE);
+      } else {
+        return referenceQueue.remove();
+      }
+    } catch (InterruptedException ex) {
+      return null;
+    }
+  }
+
+  /** If the current processor has no pending items, it deactivates it. */
+  @CompilerDirectives.TruffleBoundary
+  private synchronized void shutdownProcessorIfNoPending(ProcessItems p) {
+    assert Thread.currentThread() == p.workerThread;
+    if (processor == p && pendingItems.isEmpty()) {
+      processor = null;
+    }
+  }
+
+  /** Verifies whether given processor is still active. */
+  @CompilerDirectives.TruffleBoundary
+  private synchronized boolean isActive(ProcessItems p) {
+    return processor == p;
   }
 
   /**
@@ -152,26 +235,38 @@ public final class ResourceManager {
    * in {@link #perform} method inside of Enso execution context.
    */
   private final class ProcessItems extends ThreadLocalAction implements Runnable {
-    /**
-     * @GuardedBy("pendingItems")
-     */
-    private final List<Item> pendingItems = new ArrayList<>();
+    private final Thread workerThread;
 
     /**
-     * @GuardedBy("pendingItems")
+     * @GuardedBy("toFinalize")
      */
-    private Future<Void> request;
+    private final List<Item> toFinalize = new ArrayList<>();
 
-    private volatile boolean killed = false;
+    /**
+     * @GuardedBy("toFinalize")
+     */
+    private Future<Void> safepointRequest;
 
-    ProcessItems() {
+    ProcessItems(Function<Runnable, Thread> threadFactory) {
       super(false, false, true);
+      if (threadFactory != null) {
+        this.workerThread = threadFactory.apply(this);
+        this.workerThread.start();
+      } else {
+        this.workerThread = null;
+      }
+    }
+
+    /** Is this processor still active */
+    final boolean isActive() {
+      assert workerThread != null;
+      return ResourceManager.this.isActive(this);
     }
 
     /**
      * Runs at a safe point in middle of regular Enso program execution. Gathers all available
-     * {@link #pendingItems} and runs their finalizers. Removes all processed items from {@link
-     * #pendingItems}. If there are any remaining, continues processing them. Otherwise finishes.
+     * {@link #toFinalize} and runs their finalizers. Removes all processed items from {@link
+     * #toFinalize}. If there are any remaining, continues processing them. Otherwise finishes.
      *
      * @param access not used for anything
      */
@@ -180,27 +275,27 @@ public final class ResourceManager {
       var isMyThreadChoosen = false;
       for (; ; ) {
         Item[] toProcess;
-        synchronized (pendingItems) {
+        synchronized (toFinalize) {
           if (!isMyThreadChoosen) {
-            if (request == null || request.isCancelled()) {
-              // some thread is already handing the request
+            if (safepointRequest == null || safepointRequest.isCancelled()) {
+              // some thread is already handing the safepointRequest
               return;
             } else {
-              // I am choosen and I will loop and process pendingItems
+              // I am choosen and I will loop and process lastProcessor
               // until they are available
               isMyThreadChoosen = true;
-              // signal others this request has choosen thread
-              request.cancel(false);
+              // signal others this safepointRequest has choosen thread
+              safepointRequest.cancel(false);
             }
           }
-          if (pendingItems.isEmpty()) {
+          if (toFinalize.isEmpty()) {
             // nothing to process anymore,
-            // signal request is finished and new one shall be scheduled
-            request = null;
+            // signal safepointRequest is finished and new one shall be scheduled
+            safepointRequest = null;
             return;
           }
-          toProcess = pendingItems.toArray(Item[]::new);
-          pendingItems.clear();
+          toProcess = toFinalize.toArray(Item[]::new);
+          toFinalize.clear();
         }
         for (var it : toProcess) {
           it.finalizeNow(context);
@@ -212,44 +307,54 @@ public final class ResourceManager {
     /**
      * Running in its own thread. Waiting for {@link #referenceQueue} to be populated with GCed
      * items. Scheduling {@link #perform} action at safe points while passing the {@link Item}s to
-     * it via {@link #pendingItems}.
+     * it via {@link #toFinalize}.
      */
     @Override
     public void run() {
       while (true) {
-        try {
-          Reference<? extends ManagedResource> ref = referenceQueue.remove();
-          if (!killed) {
-            if (ref instanceof Item it) {
-              it.flaggedForFinalization.set(true);
-              synchronized (pendingItems) {
-                if (request == null) {
-                  request = context.submitThreadLocal(null, this);
-                }
-                pendingItems.add(it);
-              }
+        if (!isActive()) {
+          return;
+        }
+        var ref = removeNextQueuedItem(this);
+        if (ref instanceof Item it) {
+          it.flaggedForFinalization.set(true);
+          synchronized (toFinalize) {
+            if (safepointRequest == null) {
+              safepointRequest = context.submitThreadLocal(null, this);
             }
+            toFinalize.add(it);
           }
-          if (killed) {
-            return;
-          }
-        } catch (InterruptedException e) {
-          if (killed) {
-            return;
-          }
+          removeFromItems(it);
+        } else {
+          shutdownProcessorIfNoPending(this);
         }
       }
     }
 
+    /** Awakes the associated {@link #workerThread} by interrupting it. */
+    void awake() {
+      if (workerThread != null) {
+        workerThread.interrupt();
+      }
+    }
+
     /**
-     * Sets the killed flag of this thread. This flag being set to {@code true} will force it to
-     * stop execution at the soonest possible safe point. Other than setting this flag, the thread
-     * should also be interrupted to read it, in case it is blocked on an interruptible operation.
+     * Awaits shutdown of the worker thread. Can only be called when this processor is no longer
+     * active.
      *
-     * @param killed whether the thread should stop execution upon reading the flag.
+     * @return the list of items that deserve to be finalized
      */
-    void setKilled(boolean killed) {
-      this.killed = killed;
+    Collection<Item> awaitShutdown() {
+      assert !isActive() : "Ready to shutdown";
+      assert Thread.currentThread() != workerThread : "Cannot shutdown own thread";
+      awake();
+      while (workerThread.isAlive()) {
+        try {
+          workerThread.join();
+        } catch (InterruptedException ex) {
+        }
+      }
+      return toFinalize;
     }
   }