diff --git a/src/rollup/plugins/externals.ts b/src/rollup/plugins/externals.ts
index 8772732e52..01cd39143a 100644
--- a/src/rollup/plugins/externals.ts
+++ b/src/rollup/plugins/externals.ts
@@ -183,7 +183,7 @@ export function externals (opts: NodeExternalsOptions): Plugin {
           const isNewer = semver.gt(v2, v1)
 
           // Warn about major version differences
-          const getMajor = v => v.split('.').filter(s => s !== '0')[0]
+          const getMajor = (v: string) => v.split('.').filter(s => s !== '0')[0]
           if (getMajor(v1) !== getMajor(v2)) {
             const warn = `Multiple major versions of package \`${pkgName}\` are being externalized. Picking latest version:\n\n` + [
               `  ${isNewer ? '-' : '+'} ` + existingPkgDir + '@' + v1,
@@ -195,13 +195,14 @@ export function externals (opts: NodeExternalsOptions): Plugin {
             }
           }
 
-          // Exclude older version files
-          if (isNewer) {
-            ignoreDirs.push(existingPkgDir)
-          } else {
-            ignoreDirs.push(pkgDir)
-            pkgDir = existingPkgDir // Update for tracedPackages
+          const [newerDir, olderDir] = isNewer ? [pkgDir, existingPkgDir] : [existingPkgDir, pkgDir]
+          // Try to map traced files from one package to another for minor/patch versions
+          if (getMajor(v1) === getMajor(v2)) {
+            tracedFiles = tracedFiles.map(f => f.startsWith(olderDir + '/') ? f.replace(olderDir, newerDir) : f)
           }
+          // Exclude older version files
+          ignoreDirs.push(olderDir + '/')
+          pkgDir = newerDir // Update for tracedPackages
         }
 
         // Add to traced packages
@@ -224,9 +225,13 @@ export function externals (opts: NodeExternalsOptions): Plugin {
         if (!await isFile(file)) { return }
         const src = resolve(opts.traceOptions.base, file)
         const { pkgName, subpath } = parseNodeModulePath(file)
-        const dst = resolve(opts.outDir, `node_modules/${pkgName}/${subpath}`)
+        const dst = resolve(opts.outDir, `node_modules/${pkgName + subpath}`)
         await fsp.mkdir(dirname(dst), { recursive: true })
-        await fsp.copyFile(src, dst)
+        try {
+          await fsp.copyFile(src, dst)
+        } catch (err) {
+          consola.warn(`Could not resolve \`${src}\`. Skipping.`)
+        }
       }
 
       // Write traced files
diff --git a/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/index.mjs b/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/index.mjs
index ff603d7009..c9e08004a5 100644
--- a/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/index.mjs
+++ b/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/index.mjs
@@ -1 +1 @@
-export default '2.0.0';
+export default '2.0.1';
diff --git a/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/package.json b/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/package.json
index 35693047a5..bfb99596eb 100644
--- a/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/package.json
+++ b/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/package.json
@@ -1,5 +1,8 @@
 {
   "name": "nitro-lib",
-  "version": "2.0.0",
-  "exports": "./index.mjs"
+  "version": "2.0.1",
+  "exports": {
+    ".": "./index.mjs",
+    "./subpath": "./subpath.mjs"
+  }
 }
diff --git a/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/subpath.mjs b/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/subpath.mjs
new file mode 100644
index 0000000000..c9e08004a5
--- /dev/null
+++ b/test/fixture/_/node_modules/nitro-dep-b/node_modules/nitro-lib/subpath.mjs
@@ -0,0 +1 @@
+export default '2.0.1';
diff --git a/test/fixture/_/node_modules/nitro-lib/index.mjs b/test/fixture/_/node_modules/nitro-lib/index.mjs
index c9e08004a5..ff603d7009 100644
--- a/test/fixture/_/node_modules/nitro-lib/index.mjs
+++ b/test/fixture/_/node_modules/nitro-lib/index.mjs
@@ -1 +1 @@
-export default '2.0.1';
+export default '2.0.0';
diff --git a/test/fixture/_/node_modules/nitro-lib/package.json b/test/fixture/_/node_modules/nitro-lib/package.json
index 2163d64469..81618a9dc9 100644
--- a/test/fixture/_/node_modules/nitro-lib/package.json
+++ b/test/fixture/_/node_modules/nitro-lib/package.json
@@ -1,5 +1,8 @@
 {
   "name": "nitro-lib",
-  "version": "2.0.1",
-  "exports": "./index.mjs"
+  "version": "2.0.0",
+  "exports": {
+    ".": "./index.mjs",
+    "./subpath": "./subpath.mjs"
+  }
 }
diff --git a/test/fixture/_/node_modules/nitro-lib/subpath.mjs b/test/fixture/_/node_modules/nitro-lib/subpath.mjs
new file mode 100644
index 0000000000..ff603d7009
--- /dev/null
+++ b/test/fixture/_/node_modules/nitro-lib/subpath.mjs
@@ -0,0 +1 @@
+export default '2.0.0';
diff --git a/test/fixture/routes/modules.ts b/test/fixture/routes/modules.ts
index dc7c27e7a1..8231219c07 100644
--- a/test/fixture/routes/modules.ts
+++ b/test/fixture/routes/modules.ts
@@ -4,11 +4,14 @@ import depA from 'nitro-dep-a'
 import depB from 'nitro-dep-b'
 // @ts-ignore
 import depLib from 'nitro-lib'
+// @ts-ignore
+import subpathLib from 'nitro-lib/subpath'
 
 export default defineEventHandler(() => {
   return {
     depA,
     depB,
-    depLib
+    depLib,
+    subpathLib
   }
 })
diff --git a/test/tests.ts b/test/tests.ts
index 396b05eba0..6edacb53f9 100644
--- a/test/tests.ts
+++ b/test/tests.ts
@@ -185,7 +185,7 @@ export function testNitro (ctx: Context, getHandler: () => TestHandler | Promise
 
     it('resolve module version conflicts', async () => {
       const { data } = await callHandler({ url: '/modules' })
-      expect(data).toMatchObject({ depA: '2.0.1', depB: '2.0.1', depLib: '2.0.1' })
+      expect(data).toMatchObject({ depA: '2.0.1', depB: '2.0.1', depLib: '2.0.1', subpathLib: '2.0.1' })
     })
   }
 }