diff --git a/packages/core/build/flecks.js b/packages/core/build/flecks.js
index 656e4cb..efeb00a 100644
--- a/packages/core/build/flecks.js
+++ b/packages/core/build/flecks.js
@@ -116,6 +116,10 @@ class Flecks {
     for (let i = 0; i < flecks.length; i++) {
       this.configureFleckDefaults(flecks[i]);
     }
+    this.config = {
+      ...this.bootstrappedConfig,
+      ...this.config,
+    };
   }
 
   /**
diff --git a/packages/server/test/server/runtime-config-bootstrap.js b/packages/server/test/server/runtime-config-bootstrap.js
index 70198ab..ee70925 100644
--- a/packages/server/test/server/runtime-config-bootstrap.js
+++ b/packages/server/test/server/runtime-config-bootstrap.js
@@ -1,14 +1,37 @@
+import {mkdir, writeFile} from 'fs/promises';
+import {join} from 'path';
+
 import {expect} from 'chai';
 
 import {build, createApplication, serverActions} from './build/build';
 
 it('propagates bootstrap config', async () => {
   const path = await createApplication();
+  await mkdir(join(path, 'server-only', 'build'), {recursive: true});
+  await writeFile(join(path, 'server-only', 'package.json'), '{}');
+  const config = `
+  exports.hooks = {
+    '@flecks/core.config': () => ({
+      foo: 'bar',
+    }),
+  };
+  `;
+  await writeFile(join(path, 'server-only', 'build', 'flecks.bootstrap.js'), config);
+  await writeFile(
+    join(path, 'build', 'flecks.yml'),
+    `
+      '@flecks/build': {}
+      '@flecks/core': {}
+      '@flecks/server': {}
+      'comm:./comm': {}
+      'server-only:./server-only': {}
+    `,
+  );
   await build(path, {args: ['-d']});
-  const {results: [{payload: id}]} = await serverActions(path, [
-    {type: 'config.get', payload: '@flecks/core.id'},
+  const {results: [{payload: foo}]} = await serverActions(path, [
+    {type: 'config.get', payload: 'server-only.foo'},
     {type: 'exit'},
   ]);
-  expect(id)
-    .to.equal('flecks');
+  expect(foo)
+    .to.equal('bar');
 });