diff --git a/.changeset/lucky-chairs-begin.md b/.changeset/lucky-chairs-begin.md
new file mode 100644
index 0000000000..b2c93cc29f
--- /dev/null
+++ b/.changeset/lucky-chairs-begin.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/npm-resolver": patch
+"pnpm": patch
+---
+
+Deduplicate direct dependencies, when `resolution-mode` is set to `lowest-direct` [#6042](https://github.com/pnpm/pnpm/issues/6042).
diff --git a/pkg-manager/core/test/install/dedupeInWorkspace.ts b/pkg-manager/core/test/install/dedupeInWorkspace.ts
index 0677cc1400..dfa41799fc 100644
--- a/pkg-manager/core/test/install/dedupeInWorkspace.ts
+++ b/pkg-manager/core/test/install/dedupeInWorkspace.ts
@@ -5,7 +5,7 @@ import { mutateModules, type MutatedProject } from '@pnpm/core'
 import { addDistTag } from '@pnpm/registry-mock'
 import { testDefaults } from '../utils'
 
-test('pick common range for a dependency used in two workspace projects', async () => {
+test('pick common range for a dependency used in two workspace projects when resolution mode is highest', async () => {
   await addDistTag({ package: '@pnpm.e2e/dep-of-pkg-with-1-dep', version: '100.1.0', distTag: 'latest' })
   preparePackages([
     {
@@ -54,10 +54,67 @@ test('pick common range for a dependency used in two workspace projects', async
       rootDir: path.resolve('project-2'),
     },
   ]
-  await mutateModules(importers, await testDefaults({ allProjects, lockfileOnly: true }))
+  await mutateModules(importers, await testDefaults({ allProjects, lockfileOnly: true, resolutionMode: 'highest' }))
 
   const project = assertProject(process.cwd())
   const lockfile = await project.readLockfile()
   expect(lockfile.packages).toHaveProperty(['/@pnpm.e2e/dep-of-pkg-with-1-dep@100.0.0'])
   expect(lockfile.packages).not.toHaveProperty(['/@pnpm.e2e/dep-of-pkg-with-1-dep@100.1.0'])
 })
+
+test('pick common range for a dependency used in two workspace projects when resolution mode is lowest-direct', async () => {
+  await addDistTag({ package: '@pnpm.e2e/dep-of-pkg-with-1-dep', version: '100.1.0', distTag: 'latest' })
+  preparePackages([
+    {
+      location: 'project-1',
+      package: { name: 'project-1' },
+    },
+    {
+      location: 'project-2',
+      package: { name: 'project-2' },
+    },
+  ])
+
+  const importers: MutatedProject[] = [
+    {
+      mutation: 'install',
+      rootDir: path.resolve('project-1'),
+    },
+    {
+      mutation: 'install',
+      rootDir: path.resolve('project-2'),
+    },
+  ]
+  const allProjects = [
+    {
+      buildIndex: 0,
+      manifest: {
+        name: 'project-1',
+        version: '1.0.0',
+
+        dependencies: {
+          '@pnpm.e2e/dep-of-pkg-with-1-dep': '100.1.0',
+        },
+      },
+      rootDir: path.resolve('project-1'),
+    },
+    {
+      buildIndex: 0,
+      manifest: {
+        name: 'project-2',
+        version: '1.0.0',
+
+        dependencies: {
+          '@pnpm.e2e/dep-of-pkg-with-1-dep': '^100.0.0',
+        },
+      },
+      rootDir: path.resolve('project-2'),
+    },
+  ]
+  await mutateModules(importers, await testDefaults({ allProjects, lockfileOnly: true, resolutionMode: 'lowest-direct' }))
+
+  const project = assertProject(process.cwd())
+  const lockfile = await project.readLockfile()
+  expect(lockfile.packages).toHaveProperty(['/@pnpm.e2e/dep-of-pkg-with-1-dep@100.1.0'])
+  expect(lockfile.packages).not.toHaveProperty(['/@pnpm.e2e/dep-of-pkg-with-1-dep@100.0.0'])
+})
diff --git a/resolving/npm-resolver/src/pickPackageFromMeta.ts b/resolving/npm-resolver/src/pickPackageFromMeta.ts
index b6ab1d5d44..6d90e35350 100644
--- a/resolving/npm-resolver/src/pickPackageFromMeta.ts
+++ b/resolving/npm-resolver/src/pickPackageFromMeta.ts
@@ -60,8 +60,18 @@ export function pickPackageFromMeta (
 
 export function pickLowestVersionByVersionRange (
   meta: PackageMeta,
-  versionRange: string
+  versionRange: string,
+  preferredVerSels?: VersionSelectors
 ) {
+  if (preferredVerSels != null && Object.keys(preferredVerSels).length > 0) {
+    const prioritizedPreferredVersions = prioritizePreferredVersions(meta, versionRange, preferredVerSels)
+    for (const preferredVersions of prioritizedPreferredVersions) {
+      const preferredVersion = semver.minSatisfying(preferredVersions, versionRange, true)
+      if (preferredVersion) {
+        return preferredVersion
+      }
+    }
+  }
   if (versionRange === '*') {
     return Object.keys(meta.versions).sort(semver.compare)[0]
   }