diff --git a/.changes/migrate-plugins.md b/.changes/migrate-plugins.md
new file mode 100644
index 000000000..b9a979579
--- /dev/null
+++ b/.changes/migrate-plugins.md
@@ -0,0 +1,6 @@
+---
+"tauri-cli": patch:bug
+"@tauri-apps/cli": patch:bug
+---
+
+Migrate v1 plugins to their v2 releases.
diff --git a/.changes/migrate-prevent-duplications.md b/.changes/migrate-prevent-duplications.md
new file mode 100644
index 000000000..0edf2f3af
--- /dev/null
+++ b/.changes/migrate-prevent-duplications.md
@@ -0,0 +1,6 @@
+---
+"tauri-cli": patch:bug
+"@tauri-apps/cli": patch:bug
+---
+
+Prevent duplicate permissions on v1 migration.
diff --git a/tooling/cli/src/add.rs b/tooling/cli/src/add.rs
index e5309780e..08635c589 100644
--- a/tooling/cli/src/add.rs
+++ b/tooling/cli/src/add.rs
@@ -39,7 +39,10 @@ pub struct Options {
 
 pub fn command(options: Options) -> Result<()> {
   crate::helpers::app_paths::resolve();
+  run(options)
+}
 
+pub fn run(options: Options) -> Result<()> {
   let (plugin, version) = options
     .plugin
     .split_once('@')
diff --git a/tooling/cli/src/migrate/migrations/v1/config.rs b/tooling/cli/src/migrate/migrations/v1/config.rs
index 6722e67f2..af60d3d02 100644
--- a/tooling/cli/src/migrate/migrations/v1/config.rs
+++ b/tooling/cli/src/migrate/migrations/v1/config.rs
@@ -386,13 +386,16 @@ fn allowlist_to_permissions(
   allowlist: tauri_utils_v1::config::AllowlistConfig,
 ) -> Vec<PermissionEntry> {
   macro_rules! permissions {
-    ($allowlist: ident, $permissions_list: ident, $object: ident, $field: ident => $associated_permission: expr) => {
+    ($allowlist: ident, $permissions_list: ident, $object: ident, $field: ident => $associated_permission: expr) => {{
       if $allowlist.all || $allowlist.$object.all || $allowlist.$object.$field {
         $permissions_list.push(PermissionEntry::PermissionRef(
           $associated_permission.to_string().try_into().unwrap(),
         ));
+        true
+      } else {
+        false
       }
-    };
+    }};
   }
 
   let mut permissions = Vec::new();
@@ -474,8 +477,11 @@ fn allowlist_to_permissions(
 
   // shell
   if allowlist.shell.scope.0.is_empty() {
-    permissions!(allowlist, permissions, shell, execute => "shell:allow-execute");
-    permissions!(allowlist, permissions, shell, sidecar => "shell:allow-execute");
+    let added = permissions!(allowlist, permissions, shell, execute => "shell:allow-execute");
+    // prevent duplicated permission
+    if !added {
+      permissions!(allowlist, permissions, shell, sidecar => "shell:allow-execute");
+    }
   } else {
     let allowed = allowlist
       .shell
diff --git a/tooling/cli/src/migrate/migrations/v1/manifest.rs b/tooling/cli/src/migrate/migrations/v1/manifest.rs
index 44bad7aa4..73acd1111 100644
--- a/tooling/cli/src/migrate/migrations/v1/manifest.rs
+++ b/tooling/cli/src/migrate/migrations/v1/manifest.rs
@@ -45,6 +45,22 @@ fn migrate_manifest(manifest: &mut Document) -> Result<()> {
     ("tauri-codegen", "dependencies"),
     ("tauri-macros", "dependencies"),
     ("tauri-runtime-wry", "dependencies"),
+    // normal deps - plugins
+    ("tauri-plugin-authenticator", "dependencies"),
+    ("tauri-plugin-autostart", "dependencies"),
+    ("tauri-plugin-fs-extra", "dependencies"),
+    ("tauri-plugin-fs-watch", "dependencies"),
+    ("tauri-plugin-localhost", "dependencies"),
+    ("tauri-plugin-log", "dependencies"),
+    ("tauri-plugin-persisted-scope", "dependencies"),
+    ("tauri-plugin-positioner", "dependencies"),
+    ("tauri-plugin-single-instance", "dependencies"),
+    ("tauri-plugin-sql", "dependencies"),
+    ("tauri-plugin-store", "dependencies"),
+    ("tauri-plugin-stronghold", "dependencies"),
+    ("tauri-plugin-upload", "dependencies"),
+    ("tauri-plugin-websocket", "dependencies"),
+    ("tauri-plugin-window-state", "dependencies"),
     // dev
     ("tauri", "dev-dependencies"),
     ("tauri-utils", "dev-dependencies"),
@@ -207,6 +223,10 @@ fn migrate_dependency_table<D: TableLike>(
   remove: &[&str],
   rename: &[(&str, &str)],
 ) {
+  dep.remove("rev");
+  dep.remove("git");
+  dep.remove("branch");
+  dep.remove("tag");
   *dep.entry("version").or_insert(Item::None) = Item::Value(version.into());
   let manifest_features = dep.entry("features").or_insert(Item::None);
   if let Some(features_array) = manifest_features.as_array_mut() {
diff --git a/tooling/cli/src/migrate/migrations/v1/mod.rs b/tooling/cli/src/migrate/migrations/v1/mod.rs
index e378ab35a..26a7b7b20 100644
--- a/tooling/cli/src/migrate/migrations/v1/mod.rs
+++ b/tooling/cli/src/migrate/migrations/v1/mod.rs
@@ -25,7 +25,7 @@ pub fn run() -> Result<()> {
 
   // Add plugins
   for plugin in migrated.plugins {
-    crate::add::command(crate::add::Options {
+    crate::add::run(crate::add::Options {
       plugin: plugin.clone(),
       branch: None,
       tag: None,