diff --git a/workspaces/libnpmexec/lib/index.js b/workspaces/libnpmexec/lib/index.js
index 79d3cc1512f8e..3d9d24469ac59 100644
--- a/workspaces/libnpmexec/lib/index.js
+++ b/workspaces/libnpmexec/lib/index.js
@@ -32,7 +32,7 @@ const getManifest = async (spec, flatOptions) => {
 
 // Returns the required manifest if the spec is missing from the tree
 // Returns the found node if it is in the tree
-const missingFromTree = async ({ spec, tree, flatOptions, isNpxTree }) => {
+const missingFromTree = async ({ spec, tree, flatOptions, isNpxTree, shallow }) => {
   // If asking for a spec by name only (spec.raw === spec.name):
   //  - In local or global mode go with anything in the tree that matches
   //  - If looking in the npx cache check if a newer version is available
@@ -41,6 +41,10 @@ const missingFromTree = async ({ spec, tree, flatOptions, isNpxTree }) => {
     // registry spec that is not a specific tag.
     const nodesBySpec = tree.inventory.query('packageName', spec.name)
     for (const node of nodesBySpec) {
+      // continue if node is not a top level node
+      if (shallow && node.depth) {
+        continue
+      }
       if (spec.rawSpec === '*') {
         return { node }
       }
@@ -202,7 +206,7 @@ const exec = async (opts) => {
       const globalArb = new Arborist({ ...flatOptions, path: globalPath, global: true })
       const globalTree = await globalArb.loadActual()
       const { manifest: globalManifest } =
-        await missingFromTree({ spec, tree: globalTree, flatOptions })
+        await missingFromTree({ spec, tree: globalTree, flatOptions, shallow: true })
       if (!globalManifest && await fileExists(`${globalBin}/${args[0]}`)) {
         binPaths.push(globalBin)
         return await run()
diff --git a/workspaces/libnpmexec/test/registry.js b/workspaces/libnpmexec/test/registry.js
index 8af792018c954..81c5f90bb2b4e 100644
--- a/workspaces/libnpmexec/test/registry.js
+++ b/workspaces/libnpmexec/test/registry.js
@@ -164,3 +164,65 @@ t.test('run multiple from registry', async t => {
     value: 'packages-2.0.0',
   })
 })
+t.test('packages with different versions in the global tree', async t => {
+  const pkgA1 = createPkg({
+    localVersion: '1.0.0',
+    versions: ['1.0.0', '2.0.0'],
+    name: '@npmcli/A',
+  })
+
+  const pkgA2 = createPkg({
+    localVersion: '2.0.0',
+    name: '@npmcli/A',
+    versions: ['1.0.0', '2.0.0'],
+  })
+
+  const pkgB = createPkg({
+    localVersion: '1.0.0',
+    name: '@npmcli/B',
+  })
+
+  const pkgBfix = merge(pkgB.fixtures, {
+    node_modules: {
+      '@npmcli': { B: {
+        node_modules: {
+          '@npmcli': {
+            A: pkgA2.fixtures.packages['@npmcli-A-2.0.0'],
+          } },
+        'package.json': { dependencies: { '@npmcli/A': '2.0.0' } },
+      },
+      },
+    } })
+
+  const { chmod, exec, readOutput, binLinks, registry, path } = setup(t, {
+    pkg: [pkgA2.pkg, pkgA1.pkg, pkgB.pkg],
+    global: true,
+    testdir: merge(pkgA1.fixtures, pkgBfix),
+  })
+
+  await chmod()
+  await binLinks()
+
+  await pkgA2.package({ registry, path, times: 2, tarballs: ['2.0.0'] })
+  await pkgA1.package({ registry, path, times: 1, tarballs: [] })
+
+  await exec({
+    args: ['@npmcli/A@2.0.0'],
+  })
+
+  t.match(await readOutput('@npmcli-A'), {
+    value: 'packages-2.0.0',
+    args: [],
+    created: 'packages/@npmcli-A-2.0.0/bin-file.js',
+  })
+
+  await exec({
+    args: ['@npmcli/A@1.0.0'],
+  })
+
+  t.match(await readOutput('@npmcli-A'), {
+    value: 'local-1.0.0',
+    args: [],
+    created: 'global/node_modules/@npmcli/A/bin-file.js',
+  })
+})