diff --git a/.changeset/polite-bulldogs-repeat.md b/.changeset/polite-bulldogs-repeat.md
index 0b22398a55..32264b80c1 100644
--- a/.changeset/polite-bulldogs-repeat.md
+++ b/.changeset/polite-bulldogs-repeat.md
@@ -9,3 +9,5 @@ Renamed the `backstage-cli migrate package-role` command to `backstage-cli migra
 Updated the package role definitions by renaming `plugin-frontend` to `frontend-plugin`, as well as the same reshuffle to `frontend-plugin-module`, `backend-plugin`, and `backend-plugin-module`.
 
 The `backstage-cli migrate package-scripts` received several tweaks to make it more accurate. It now tries to maintain existing script arguments, like `--config` parameters for `build` and `start` scripts.
+
+The `backstage-cli script build` command set an incorrect target directory for `app` and `backend` packages, which has been fixed.
diff --git a/packages/cli/src/commands/build/buildBackend.ts b/packages/cli/src/commands/build/buildBackend.ts
index e32b7956db..0768728f00 100644
--- a/packages/cli/src/commands/build/buildBackend.ts
+++ b/packages/cli/src/commands/build/buildBackend.ts
@@ -49,19 +49,20 @@ export async function buildBackend(options: BuildBackendOptions) {
 
     // We built the target backend package using the regular build process, but the result of
     // that has now been packed into the dist workspace, so clean up the dist dir.
-    await fs.remove(targetDir);
-    await fs.mkdir(targetDir);
+    const distDir = resolvePath(targetDir, 'dist');
+    await fs.remove(distDir);
+    await fs.mkdir(distDir);
 
     // Move out skeleton.tar.gz before we create the main bundle, no point having that included up twice.
     await fs.move(
       resolvePath(tmpDir, SKELETON_FILE),
-      resolvePath(targetDir, SKELETON_FILE),
+      resolvePath(distDir, SKELETON_FILE),
     );
 
     // Create main bundle.tar.gz, with some tweaks to make it more likely hit Docker build cache.
     await tar.create(
       {
-        file: resolvePath(targetDir, BUNDLE_FILE),
+        file: resolvePath(distDir, BUNDLE_FILE),
         cwd: tmpDir,
         portable: true,
         noMtime: true,
diff --git a/packages/cli/src/commands/build/command.ts b/packages/cli/src/commands/build/command.ts
index 1189883b12..04b9893c31 100644
--- a/packages/cli/src/commands/build/command.ts
+++ b/packages/cli/src/commands/build/command.ts
@@ -26,14 +26,14 @@ export async function command(cmd: Command): Promise<void> {
 
   if (role === 'app') {
     return buildApp({
-      targetDir: paths.resolveTarget('dist'),
+      targetDir: paths.targetDir,
       configPaths: cmd.config as string[],
       writeStats: Boolean(cmd.stats),
     });
   }
   if (role === 'backend') {
     return buildBackend({
-      targetDir: paths.resolveTarget('dist'),
+      targetDir: paths.targetDir,
       skipBuildDependencies: Boolean(cmd.skipBuildDependencies),
     });
   }