diff --git a/scripts/build-desktop-artifact.test.ts b/scripts/build-desktop-artifact.test.ts
index 345217a540..8dc23484ab 100644
--- a/scripts/build-desktop-artifact.test.ts
+++ b/scripts/build-desktop-artifact.test.ts
@@ -65,19 +65,37 @@ it.layer(NodeServices.layer)("build-desktop-artifact", (it) => {
     );
   });
 
-  it("carries workspace patch metadata into staged desktop installs", () => {
+  it("carries only staged dependency patch metadata into staged desktop installs", () => {
     assert.deepStrictEqual(
-      createStagePnpmConfig({
-        "@pierre/diffs@1.1.20": "patches/@pierre%2Fdiffs@1.1.20.patch",
-      }),
+      createStagePnpmConfig(
+        {
+          "@expo/metro-config@56.0.13": "patches/@expo%2Fmetro-config@56.0.13.patch",
+          "@pierre/diffs@1.1.20": "patches/@pierre%2Fdiffs@1.1.20.patch",
+          "alchemy@2.0.0-beta.49": "patches/alchemy@2.0.0-beta.49.patch",
+          "effect@4.0.0-beta.73": "patches/effect@4.0.0-beta.73.patch",
+        },
+        {
+          "@pierre/diffs": "1.1.20",
+          effect: "4.0.0-beta.73",
+        },
+      ),
       {
         patchedDependencies: {
           "@pierre/diffs@1.1.20": "patches/@pierre%2Fdiffs@1.1.20.patch",
+          "effect@4.0.0-beta.73": "patches/effect@4.0.0-beta.73.patch",
         },
       },
     );
 
-    assert.equal(createStagePnpmConfig({}), undefined);
+    assert.equal(
+      createStagePnpmConfig(
+        {
+          "@expo/metro-config@56.0.13": "patches/@expo%2Fmetro-config@56.0.13.patch",
+        },
+        { effect: "4.0.0-beta.73" },
+      ),
+      undefined,
+    );
   });
 
   it("falls back to the default mock update port when the configured port is blank", () => {
diff --git a/scripts/build-desktop-artifact.ts b/scripts/build-desktop-artifact.ts
index 53f7da8e69..f86c94e5d9 100644
--- a/scripts/build-desktop-artifact.ts
+++ b/scripts/build-desktop-artifact.ts
@@ -278,8 +278,22 @@ interface StagePackageJson {
 
 export function createStagePnpmConfig(
   patchedDependencies: Record<string, string>,
+  dependencies: Record<string, unknown>,
 ): StagePackageJson["pnpm"] | undefined {
-  return Object.keys(patchedDependencies).length > 0 ? { patchedDependencies } : undefined;
+  const stagePatchedDependencies = Object.fromEntries(
+    Object.entries(patchedDependencies).filter(([patchKey]) =>
+      Object.hasOwn(dependencies, getPatchedDependencyPackageName(patchKey)),
+    ),
+  );
+
+  return Object.keys(stagePatchedDependencies).length > 0
+    ? { patchedDependencies: stagePatchedDependencies }
+    : undefined;
+}
+
+function getPatchedDependencyPackageName(patchKey: string): string {
+  const versionSeparator = patchKey.lastIndexOf("@");
+  return versionSeparator > 0 ? patchKey.slice(0, versionSeparator) : patchKey;
 }
 
 const AzureTrustedSigningOptionsConfig = Config.all({
@@ -878,7 +892,11 @@ const buildDesktopArtifact = Effect.fn("buildDesktopArtifact")(function* (
   // electron-builder is filtering out stageResourcesDir directory in the AppImage for production
   yield* fs.copy(stageResourcesDir, path.join(stageAppDir, "apps/desktop/prod-resources"));
 
-  const stagePnpmConfig = createStagePnpmConfig(workspacePatchedDependencies);
+  const stageDependencies = {
+    ...resolvedServerDependencies,
+    ...resolvedDesktopRuntimeDependencies,
+  };
+  const stagePnpmConfig = createStagePnpmConfig(workspacePatchedDependencies, stageDependencies);
   const stagePackageJson: StagePackageJson = {
     name: "t3code",
     version: appVersion,
@@ -897,10 +915,7 @@ const buildDesktopArtifact = Effect.fn("buildDesktopArtifact")(function* (
       options.mockUpdates,
       options.mockUpdateServerPort,
     ),
-    dependencies: {
-      ...resolvedServerDependencies,
-      ...resolvedDesktopRuntimeDependencies,
-    },
+    dependencies: stageDependencies,
     devDependencies: {
       electron: electronVersion,
     },