diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/migration_from_tsup_monorepo/snapshots/migration_from_tsup_monorepo_shared_root_config.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/migration_from_tsup_monorepo/snapshots/migration_from_tsup_monorepo_shared_root_config.md
index 739daf78ca..c8c4aec996 100644
--- a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/migration_from_tsup_monorepo/snapshots/migration_from_tsup_monorepo_shared_root_config.md
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/migration_from_tsup_monorepo/snapshots/migration_from_tsup_monorepo_shared_root_config.md
@@ -43,8 +43,6 @@ Please manually merge tsdown.config.ts into vite.config.ts, see https://viteplus
 • tsup config migrated to tsdown (`vp pack`)
 ! Warnings:
   - tsup.config.ts is shared by packages/a, packages/b. It was preserved and must be migrated manually.
-→ Manual follow-up:
-  - Please manually merge tsdown.config.ts into vite.config.ts, see https://viteplus.dev/guide/migrate#tsdown
 ```
 
 ## `vpt stat-file tsup.config.ts --assert file`
diff --git a/packages/cli/src/migration/__tests__/migrator.spec.ts b/packages/cli/src/migration/__tests__/migrator.spec.ts
index d3e92bdc6c..c395b594db 100644
--- a/packages/cli/src/migration/__tests__/migrator.spec.ts
+++ b/packages/cli/src/migration/__tests__/migrator.spec.ts
@@ -8796,6 +8796,7 @@ describe('existing Vite+ core migration finalization', () => {
       scripts: true,
       tsconfigTypes: true,
       imports: true,
+      tsdownConfig: false,
     });
 
     const pkg = readJson(path.join(tmpDir, 'package.json')) as {
@@ -8850,6 +8851,85 @@ describe('existing Vite+ core migration finalization', () => {
     };
     expect(appPkg.scripts.dev).toBe('vp dev');
   });
+
+  it('makes a leftover tsdown config discoverable in an existing Vite+ project', () => {
+    fs.writeFileSync(
+      path.join(tmpDir, 'package.json'),
+      JSON.stringify({ name: 'test', devDependencies: { 'vite-plus': 'latest' } }, null, 2),
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, 'tsdown.config.ts'),
+      `import { defineConfig } from 'tsdown';
+
+export default defineConfig({
+  entry: { index: 'src/index.ts', utils: 'src/utils.ts' },
+});
+`,
+    );
+
+    const workspaceInfo = makeWorkspaceInfo(tmpDir, PackageManager.pnpm);
+    expect(finalizeCoreMigrationForExistingVitePlus(workspaceInfo, true)).toEqual({
+      scripts: false,
+      tsconfigTypes: false,
+      imports: true,
+      tsdownConfig: true,
+    });
+    expect(fs.readFileSync(path.join(tmpDir, 'vite.config.ts'), 'utf8')).toContain(
+      "import tsdownConfig from './tsdown.config.js';",
+    );
+    expect(fs.readFileSync(path.join(tmpDir, 'vite.config.ts'), 'utf8')).toContain(
+      'pack: tsdownConfig',
+    );
+    expect(fs.readFileSync(path.join(tmpDir, 'tsdown.config.ts'), 'utf8')).toContain(
+      "from 'vite-plus/pack'",
+    );
+
+    expect(finalizeCoreMigrationForExistingVitePlus(workspaceInfo, true)).toEqual({
+      scripts: false,
+      tsconfigTypes: false,
+      imports: false,
+      tsdownConfig: false,
+    });
+  });
+
+  it('preserves a tsdown config already wired to pack under a different import name', () => {
+    fs.writeFileSync(
+      path.join(tmpDir, 'package.json'),
+      JSON.stringify({ name: 'test', devDependencies: { 'vite-plus': 'latest' } }, null, 2),
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, 'vite.config.ts'),
+      `import packConfig from './tsdown.config.js';
+
+export default { pack: packConfig({}) };
+`,
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, 'tsdown.config.ts'),
+      `import { defineConfig } from 'tsdown';
+
+export default defineConfig({ entry: 'src/index.ts' });
+`,
+    );
+
+    const originalViteConfig = fs.readFileSync(path.join(tmpDir, 'vite.config.ts'), 'utf8');
+    const report = createMigrationReport();
+    const result = finalizeCoreMigrationForExistingVitePlus(
+      makeWorkspaceInfo(tmpDir, PackageManager.pnpm),
+      true,
+      report,
+    );
+
+    expect(result).toEqual({
+      scripts: false,
+      tsconfigTypes: false,
+      imports: true,
+      tsdownConfig: false,
+    });
+    expect(fs.readFileSync(path.join(tmpDir, 'vite.config.ts'), 'utf8')).toBe(originalViteConfig);
+    expect(report.tsdownImportCount).toBe(0);
+    expect(report.manualSteps).toEqual([]);
+  });
 });
 
 // Regression: templates such as `create-fate` ship a populated vite.config.ts
diff --git a/packages/cli/src/migration/bin.ts b/packages/cli/src/migration/bin.ts
index b43647875e..ceaaa61ce8 100644
--- a/packages/cli/src/migration/bin.ts
+++ b/packages/cli/src/migration/bin.ts
@@ -1114,7 +1114,8 @@ async function main() {
     if (
       coreMigrationResult.scripts ||
       coreMigrationResult.tsconfigTypes ||
-      coreMigrationResult.imports
+      coreMigrationResult.imports ||
+      coreMigrationResult.tsdownConfig
     ) {
       didMigrate = true;
     }
diff --git a/packages/cli/src/migration/migrator/core-finalization.ts b/packages/cli/src/migration/migrator/core-finalization.ts
index 29af68a91a..46b0d51d76 100644
--- a/packages/cli/src/migration/migrator/core-finalization.ts
+++ b/packages/cli/src/migration/migrator/core-finalization.ts
@@ -5,7 +5,12 @@ import { rewriteScripts } from '../../../binding/index.js';
 import { type WorkspacePackage } from '../../types/index.ts';
 import { editJsonFile, readJsonFile } from '../../utils/json.ts';
 import { rulesDir } from '../../utils/path.ts';
-import { hasTsconfigTypesToRewrite, rewriteAllImports, rewriteTsconfigTypes } from '../migrator.ts';
+import {
+  hasTsconfigTypesToRewrite,
+  mergeTsdownConfigFile,
+  rewriteAllImports,
+  rewriteTsconfigTypes,
+} from '../migrator.ts';
 import { type MigrationReport } from '../report.ts';
 
 const RULES_YAML_PATH = path.join(rulesDir, 'vite-tools.yml');
@@ -76,6 +81,7 @@ export type CoreMigrationFinalizationResult = {
   scripts: boolean;
   tsconfigTypes: boolean;
   imports: boolean;
+  tsdownConfig: boolean;
 };
 
 function getCoreMigrationProjectPaths(workspaceInfo: CoreMigrationWorkspace): string[] {
@@ -140,6 +146,7 @@ export function finalizeCoreMigrationForExistingVitePlus(
     scripts: false,
     tsconfigTypes: false,
     imports: false,
+    tsdownConfig: false,
   };
 
   if (pending.scripts) {
@@ -157,5 +164,12 @@ export function finalizeCoreMigrationForExistingVitePlus(
 
   result.imports = rewriteAllImports(workspaceInfo.rootDir, silent, report, true);
 
+  // Partial migrations can already have a Vite+ dependency while leaving
+  // tsdown.config.* undiscoverable by vp pack. Finalize those configs on the
+  // existing-Vite+ path just as the fresh migration path does.
+  for (const projectPath of projectPaths) {
+    result.tsdownConfig = mergeTsdownConfigFile(projectPath, silent, report) || result.tsdownConfig;
+  }
+
   return result;
 }
diff --git a/packages/cli/src/migration/migrator/vite-config.ts b/packages/cli/src/migration/migrator/vite-config.ts
index 2310ba9e08..63253688cb 100644
--- a/packages/cli/src/migration/migrator/vite-config.ts
+++ b/packages/cli/src/migration/migrator/vite-config.ts
@@ -174,11 +174,12 @@ export function mergeTsdownConfigFile(
   projectPath: string,
   silent = false,
   report?: MigrationReport,
-): void {
+): boolean {
   const configs = detectConfigs(projectPath);
   if (!configs.tsdownConfig) {
-    return;
+    return false;
   }
+  const createdViteConfig = !configs.viteConfig;
   const viteConfig = ensureViteConfig(projectPath, configs, silent, report);
 
   const fullViteConfigPath = path.join(projectPath, viteConfig);
@@ -187,11 +188,34 @@ export function mergeTsdownConfigFile(
   // For JSON files, merge content directly and delete the file
   if (configs.tsdownConfig.endsWith('.json')) {
     mergeAndRemoveJsonConfig(projectPath, viteConfig, configs.tsdownConfig, 'pack', silent, report);
-    return;
+    return createdViteConfig || !fs.existsSync(fullTsdownConfigPath);
   }
 
   // For TS/JS files, import the config file
   const tsdownRelativePath = `./${configs.tsdownConfig}`;
+  // Do not prepend a second `pack` key when the config is already wired under
+  // a different local import name. If a pack config exists but does not import
+  // this tsdown config, leave both files untouched and keep the manual follow-up.
+  if (hasConfigKey(fullViteConfigPath, 'pack')) {
+    const viteConfigContent = fs.readFileSync(fullViteConfigPath, 'utf8');
+    const runtimeImportPath = tsdownRelativePath
+      .replace(/\.mts$/, '.mjs')
+      .replace(/\.cts$/, '.cjs')
+      .replace(/\.ts$/, '.js');
+    const importsTsdownConfig = [tsdownRelativePath, runtimeImportPath].some(
+      (importPath) =>
+        viteConfigContent.includes(`from '${importPath}'`) ||
+        viteConfigContent.includes(`from "${importPath}"`),
+    );
+    if (!importsTsdownConfig) {
+      infoMigration(
+        `Please manually merge ${displayRelative(fullTsdownConfigPath)} into ${displayRelative(fullViteConfigPath)}, see https://viteplus.dev/guide/migrate#tsdown`,
+        report,
+      );
+    }
+    return false;
+  }
+
   const result = mergeTsdownConfig(fullViteConfigPath, tsdownRelativePath);
   if (result.updated) {
     fs.writeFileSync(fullViteConfigPath, result.content);
@@ -209,6 +233,7 @@ export function mergeTsdownConfigFile(
     `Please manually merge ${displayRelative(fullTsdownConfigPath)} into ${displayRelative(fullViteConfigPath)}, see https://viteplus.dev/guide/migrate#tsdown`,
     report,
   );
+  return createdViteConfig || result.updated;
 }
 
 /**