diff --git a/cli/src/internal/maintenance/upgradePrestart.cjs b/cli/src/internal/maintenance/upgradePrestart.cjs
index d1815636..effbafc0 100644
--- a/cli/src/internal/maintenance/upgradePrestart.cjs
+++ b/cli/src/internal/maintenance/upgradePrestart.cjs
@@ -210,6 +210,18 @@ async function prestartBackend(
   }
 }
 
+async function cleanSqliteBuildArtifacts(directory) {
+  const names = await fs.readdir(directory).catch((error) => {
+    if (error.code !== 'ENOENT') throw error;
+    return [];
+  });
+  // node-pre-gyp's runtime copy lives in lib/binding. Its build directories
+  // retain compiler objects and an absolute node_gyp_bins/python3 symlink.
+  for (const name of names)
+    if (name === 'build' || /^build-tmp-napi-v\d+$/.test(name))
+      await fs.rm(path.join(directory, name), { recursive: true, force: true });
+}
+
 async function repairDependencies(source, { target, signal, env }) {
   const workspace = await fs.mkdtemp(
     path.join(path.dirname(source), 'repair-'),
@@ -299,8 +311,12 @@ async function repairDependencies(source, { target, signal, env }) {
       '--child-concurrency=1',
       '--network-concurrency=2',
     ]);
-    if (pkg.dependencies?.sqlite3)
+    if (pkg.dependencies?.sqlite3) {
       await run(['rebuild', 'sqlite3', '@whyour/sqlite3']);
+      await cleanSqliteBuildArtifacts(
+        path.join(workspace, 'node_modules/sqlite3'),
+      );
+    }
     if (
       !(await fs.readFile(path.join(source, 'pnpm-lock.yaml'))).equals(
         await fs.readFile(path.join(workspace, 'pnpm-lock.yaml')),
@@ -391,5 +407,6 @@ module.exports = {
   prestartBackend,
   dependencyFailure,
   repairDependencies,
+  cleanSqliteBuildArtifacts,
   probeLimits,
 };
diff --git a/scripts/rebuild-migration-sqlite.cjs b/scripts/rebuild-migration-sqlite.cjs
index f3ebf947..b5eb2ee7 100644
--- a/scripts/rebuild-migration-sqlite.cjs
+++ b/scripts/rebuild-migration-sqlite.cjs
@@ -7,7 +7,7 @@ const { createRequire } = require('node:module');
 const { execFile } = require('node:child_process');
 const { promisify } = require('node:util');
 const bundle = require('../cli/src/internal/maintenance/platformBundle.cjs');
-const { repairDependencies } = require('../cli/src/internal/maintenance/upgradePrestart.cjs');
+const { repairDependencies, cleanSqliteBuildArtifacts } = require('../cli/src/internal/maintenance/upgradePrestart.cjs');
 
 function assertArmv6Addon(attributes) {
   // Alpine's ARM CRT objects are ARMv6KZ (the ARM1176 architecture). Linking
@@ -56,9 +56,7 @@ async function rebuildMigrationSqlite(root, {
   // node-pre-gyp copies the addon to lib/binding and then renames build to
   // build-tmp-napi-v<N>. Both layouts contain compiler objects and an absolute
   // node_gyp_bins/python3 link; none belongs in a portable runtime archive.
-  for (const name of await fs.readdir(rebuilt))
-    if (name === 'build' || /^build-tmp-napi-v\d+$/.test(name))
-      await fs.rm(path.join(rebuilt, name), { recursive: true, force: true });
+  await cleanSqliteBuildArtifacts(rebuilt);
   console.log('Legacy bridge SQLite rebuilt and verified for ARMv6 hard-float');
   return true;
 }
diff --git a/test/back/upgrade-prestart.test.cjs b/test/back/upgrade-prestart.test.cjs
index 2a43525b..5d6bb6db 100644
--- a/test/back/upgrade-prestart.test.cjs
+++ b/test/back/upgrade-prestart.test.cjs
@@ -261,6 +261,76 @@ test('ARMv6 repair isolates configuration, uses frozen install, one compiler job
   assert.deepEqual((await fs.readdir(root)).sort(), ['bin', 'source']);
 });
 
+test('successful legacy repair publishes only portable runtime files from a pnpm alias', async (t) => {
+  const root = await fs.mkdtemp(path.join(os.tmpdir(), 'ql-repair-portable-'));
+  t.after(() => fs.rm(root, { recursive: true, force: true }));
+  const source = path.join(root, 'source'),
+    bin = path.join(root, 'bin');
+  const outside = path.join(root, 'outside');
+  await fs.mkdir(path.join(source, 'node_modules'), { recursive: true });
+  await fs.mkdir(bin);
+  await fs.mkdir(outside);
+  await fs.writeFile(path.join(outside, 'keep'), 'unrelated file');
+  await fs.writeFile(
+    path.join(source, 'node_modules/old'),
+    'previous dependency',
+  );
+  await fs.writeFile(
+    path.join(source, 'package.json'),
+    JSON.stringify({
+      packageManager: 'pnpm@8.3.1',
+      dependencies: { sqlite3: 'npm:@whyour/sqlite3@1.1.2' },
+    }),
+  );
+  await fs.writeFile(path.join(source, 'pnpm-lock.yaml'), 'frozen lock');
+  await fs.writeFile(
+    path.join(bin, 'pnpm'),
+    `#!${process.execPath}
+    const fs = require('node:fs');
+    if (process.argv[2] === '--version') { console.log('8.3.1'); process.exit(0); }
+    const pkg = 'node_modules/.pnpm/@whyour+sqlite3@1.1.2/node_modules/@whyour/sqlite3';
+    if (process.argv[2] === 'install') {
+      fs.mkdirSync(pkg + '/lib/binding/napi-v6-linux-arm', {recursive:true});
+      fs.writeFileSync(pkg + '/package.json', '{}');
+      fs.symlinkSync('.pnpm/@whyour+sqlite3@1.1.2/node_modules/@whyour/sqlite3', 'node_modules/sqlite3');
+    } else if (process.argv[2] === 'rebuild') {
+      fs.writeFileSync(pkg + '/lib/binding/napi-v6-linux-arm/node_sqlite3.node', 'compiled addon');
+      for (const name of ['build', 'build-tmp-napi-v6']) {
+        fs.mkdirSync(pkg + '/' + name + '/node_gyp_bins', {recursive:true});
+        fs.symlinkSync('/usr/bin/python3', pkg + '/' + name + '/node_gyp_bins/python3');
+      }
+      fs.symlinkSync(${JSON.stringify(outside)}, pkg + '/build-tmp-napi-v3');
+    } else { throw Error('unexpected command'); }
+  `,
+    { mode: 0o755 },
+  );
+  await repairDependencies(source, {
+    target: { arch: 'armv6' },
+    env: { PATH: bin },
+  });
+  const sqlite = path.join(source, 'node_modules/sqlite3');
+  assert.equal(
+    await fs.readFile(
+      path.join(sqlite, 'lib/binding/napi-v6-linux-arm/node_sqlite3.node'),
+      'utf8',
+    ),
+    'compiled addon',
+  );
+  for (const name of ['build', 'build-tmp-napi-v3', 'build-tmp-napi-v6'])
+    await assert.rejects(fs.lstat(path.join(sqlite, name)), { code: 'ENOENT' });
+  assert.equal(
+    await fs.readFile(path.join(outside, 'keep'), 'utf8'),
+    'unrelated file',
+  );
+  await assert.rejects(fs.access(path.join(source, 'node_modules/old')), {
+    code: 'ENOENT',
+  });
+  const {
+    inventory,
+  } = require('../../cli/src/internal/maintenance/platformBundle.cjs');
+  await inventory({ source });
+});
+
 test('repair classification excludes application, platform, config, database, OOM and timeouts', () => {
   for (const error of [
     { code: 'MODULE_NOT_FOUND', message: "Cannot find module './api/missing'" },