diff --git a/.changeset/chatty-coats-thank.md b/.changeset/chatty-coats-thank.md
new file mode 100644
index 0000000000..17faf43d87
--- /dev/null
+++ b/.changeset/chatty-coats-thank.md
@@ -0,0 +1,5 @@
+---
+'@backstage/cli': patch
+---
+
+Fix the build for packages with multiple entry points to avoid duplicated modules.
diff --git a/packages/cli/src/lib/builder/config.ts b/packages/cli/src/lib/builder/config.ts
index 3e61dd113a..7bd10cfcc3 100644
--- a/packages/cli/src/lib/builder/config.ts
+++ b/packages/cli/src/lib/builder/config.ts
@@ -75,117 +75,126 @@ export async function makeRollupConfigs(
   const distDir = resolvePath(targetDir, 'dist');
   const entryPoints = readEntryPoints(targetPkg);
 
-  for (const { path, name, ext } of entryPoints) {
-    if (!SCRIPT_EXTS.includes(ext)) {
-      continue;
-    }
+  const scriptEntryPoints = entryPoints.filter(e =>
+    SCRIPT_EXTS.includes(e.ext),
+  );
 
-    if (options.outputs.has(Output.cjs) || options.outputs.has(Output.esm)) {
-      const output = new Array<OutputOptions>();
-      const mainFields = ['module', 'main'];
+  if (options.outputs.has(Output.cjs) || options.outputs.has(Output.esm)) {
+    const output = new Array<OutputOptions>();
+    const mainFields = ['module', 'main'];
 
-      if (options.outputs.has(Output.cjs)) {
-        output.push({
-          dir: distDir,
-          entryFileNames: `${name}.cjs.js`,
-          chunkFileNames: `cjs/${name}/[name]-[hash].cjs.js`,
-          format: 'commonjs',
-          sourcemap: true,
-        });
-      }
-      if (options.outputs.has(Output.esm)) {
-        output.push({
-          dir: distDir,
-          entryFileNames: `${name}.esm.js`,
-          chunkFileNames: `esm/${name}/[name]-[hash].esm.js`,
-          format: 'module',
-          sourcemap: true,
-        });
-        // Assume we're building for the browser if ESM output is included
-        mainFields.unshift('browser');
-      }
-
-      configs.push({
-        input: resolvePath(targetDir, path),
-        output,
-        onwarn,
-        preserveEntrySignatures: 'strict',
-        // All module imports are always marked as external
-        external: (source, importer, isResolved) =>
-          Boolean(importer && !isResolved && !isFileImport(source)),
-        plugins: [
-          resolve({ mainFields }),
-          commonjs({
-            include: /node_modules/,
-            exclude: [/\/[^/]+\.(?:stories|test)\.[^/]+$/],
-          }),
-          postcss(),
-          forwardFileImports({
-            exclude: /\.icon\.svg$/,
-            include: [
-              /\.svg$/,
-              /\.png$/,
-              /\.gif$/,
-              /\.jpg$/,
-              /\.jpeg$/,
-              /\.eot$/,
-              /\.woff$/,
-              /\.woff2$/,
-              /\.ttf$/,
-              /\.md$/,
-            ],
-          }),
-          json(),
-          yaml(),
-          svgr({
-            include: /\.icon\.svg$/,
-            template: svgrTemplate,
-          }),
-          esbuild({
-            target: 'es2019',
-            minify: options.minify,
-          }),
-        ],
+    if (options.outputs.has(Output.cjs)) {
+      output.push({
+        dir: distDir,
+        entryFileNames: `[name].cjs.js`,
+        chunkFileNames: `cjs/[name]-[hash].cjs.js`,
+        format: 'commonjs',
+        sourcemap: true,
       });
     }
+    if (options.outputs.has(Output.esm)) {
+      output.push({
+        dir: distDir,
+        entryFileNames: `[name].esm.js`,
+        chunkFileNames: `esm/[name]-[hash].esm.js`,
+        format: 'module',
+        sourcemap: true,
+      });
+      // Assume we're building for the browser if ESM output is included
+      mainFields.unshift('browser');
+    }
 
-    if (options.outputs.has(Output.types) && !options.useApiExtractor) {
-      const typesInput = paths.resolveTargetRoot(
-        'dist-types',
-        relativePath(paths.targetRoot, targetDir),
-        path.replace(/\.ts$/, '.d.ts'),
-      );
+    configs.push({
+      input: Object.fromEntries(
+        scriptEntryPoints.map(e => [e.name, resolvePath(targetDir, e.path)]),
+      ),
+      output,
+      onwarn,
+      preserveEntrySignatures: 'strict',
+      // All module imports are always marked as external
+      external: (source, importer, isResolved) =>
+        Boolean(importer && !isResolved && !isFileImport(source)),
+      plugins: [
+        resolve({ mainFields }),
+        commonjs({
+          include: /node_modules/,
+          exclude: [/\/[^/]+\.(?:stories|test)\.[^/]+$/],
+        }),
+        postcss(),
+        forwardFileImports({
+          exclude: /\.icon\.svg$/,
+          include: [
+            /\.svg$/,
+            /\.png$/,
+            /\.gif$/,
+            /\.jpg$/,
+            /\.jpeg$/,
+            /\.eot$/,
+            /\.woff$/,
+            /\.woff2$/,
+            /\.ttf$/,
+            /\.md$/,
+          ],
+        }),
+        json(),
+        yaml(),
+        svgr({
+          include: /\.icon\.svg$/,
+          template: svgrTemplate,
+        }),
+        esbuild({
+          target: 'es2019',
+          minify: options.minify,
+        }),
+      ],
+    });
+  }
 
-      const declarationsExist = await fs.pathExists(typesInput);
+  if (options.outputs.has(Output.types) && !options.useApiExtractor) {
+    const input = Object.fromEntries(
+      scriptEntryPoints.map(e => [
+        e.name,
+        paths.resolveTargetRoot(
+          'dist-types',
+          relativePath(paths.targetRoot, targetDir),
+          e.path.replace(/\.ts$/, '.d.ts'),
+        ),
+      ]),
+    );
+
+    for (const path of Object.values(input)) {
+      const declarationsExist = await fs.pathExists(path);
       if (!declarationsExist) {
-        const declarationPath = relativePath(targetDir, typesInput);
+        const declarationPath = relativePath(targetDir, path);
         throw new Error(
           `No declaration files found at ${declarationPath}, be sure to run ${chalk.bgRed.white(
             'yarn tsc',
           )} to generate .d.ts files before packaging`,
         );
       }
-
-      configs.push({
-        input: typesInput,
-        output: {
-          file: resolvePath(distDir, `${name}.d.ts`),
-          format: 'es',
-        },
-        external: [
-          /\.css$/,
-          /\.scss$/,
-          /\.sass$/,
-          /\.svg$/,
-          /\.eot$/,
-          /\.woff$/,
-          /\.woff2$/,
-          /\.ttf$/,
-        ],
-        onwarn,
-        plugins: [dts()],
-      });
     }
+
+    configs.push({
+      input,
+      output: {
+        dir: distDir,
+        entryFileNames: `[name].d.ts`,
+        chunkFileNames: `types/[name]-[hash].d.ts`,
+        format: 'es',
+      },
+      external: [
+        /\.css$/,
+        /\.scss$/,
+        /\.sass$/,
+        /\.svg$/,
+        /\.eot$/,
+        /\.woff$/,
+        /\.woff2$/,
+        /\.ttf$/,
+      ],
+      onwarn,
+      plugins: [dts()],
+    });
   }
 
   return configs;