diff --git a/apps/server/src/keybindings.test.ts b/apps/server/src/keybindings.test.ts
index a51ad20afbe..2eef6ac8416 100644
--- a/apps/server/src/keybindings.test.ts
+++ b/apps/server/src/keybindings.test.ts
@@ -411,6 +411,28 @@ it.layer(NodeServices.layer)("keybindings", (it) => {
     }).pipe(Effect.provide(makeKeybindingsLayer())),
   );
 
+  it.effect("replacing with a rule that already exists elsewhere does not duplicate it", () =>
+    Effect.gen(function* () {
+      const { keybindingsConfigPath } = yield* ServerConfig.ServerConfig;
+      yield* writeKeybindingsConfig(keybindingsConfigPath, [
+        { key: "mod+r", command: "script.run-tests.run" },
+        { key: "mod+alt+r", command: "script.run-tests.run" },
+      ]);
+      yield* Effect.gen(function* () {
+        const keybindings = yield* Keybindings.Keybindings;
+        return yield* keybindings.upsertKeybindingRule({
+          key: "mod+alt+r",
+          command: "script.run-tests.run",
+          replace: { key: "mod+r", command: "script.run-tests.run" },
+        });
+      });
+
+      const persisted = yield* readKeybindingsConfig(keybindingsConfigPath);
+      const persistedView = persisted.map(({ key, command }) => ({ key, command }));
+      assert.deepEqual(persistedView, [{ key: "mod+alt+r", command: "script.run-tests.run" }]);
+    }).pipe(Effect.provide(makeKeybindingsLayer())),
+  );
+
   it.effect("removes only the targeted custom keybinding", () =>
     Effect.gen(function* () {
       const { keybindingsConfigPath } = yield* ServerConfig.ServerConfig;
diff --git a/apps/server/src/keybindings.ts b/apps/server/src/keybindings.ts
index 5ddae4943f8..18a78fe3623 100644
--- a/apps/server/src/keybindings.ts
+++ b/apps/server/src/keybindings.ts
@@ -644,7 +644,9 @@ const make = Effect.gen(function* () {
           const nextConfig = [
             ...customConfig.filter((entry) => {
               if (replaceTarget) {
-                return !isSameKeybindingRule(entry, replaceTarget);
+                return (
+                  !isSameKeybindingRule(entry, replaceTarget) && !isSameKeybindingRule(entry, rule)
+                );
               }
               return !isSameKeybindingRule(entry, rule);
             }),