diff --git a/.changeset/good-radios-fail.md b/.changeset/good-radios-fail.md
new file mode 100644
index 00000000000..c61c84d2ad5
--- /dev/null
+++ b/.changeset/good-radios-fail.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/npm-resolver": patch
+---
+
+fix: correctly install dependencies when resolution-mode is lowest-direct or time-based
diff --git a/pkg-manager/core/test/install/resolutionMode.ts b/pkg-manager/core/test/install/resolutionMode.ts
index f32731010c1..90837991c5d 100644
--- a/pkg-manager/core/test/install/resolutionMode.ts
+++ b/pkg-manager/core/test/install/resolutionMode.ts
@@ -92,3 +92,40 @@ test('the lowest version of a direct dependency is installed when resolution mod
     '@pnpm.e2e/pkg-with-1-dep': '^100.1.0',
   })
 })
+
+test('the lowest version of a direct dependency is installed when resolution mode is lowest-direct and already installed other version ', async () => {
+  const project = prepareEmpty()
+
+  await addDependenciesToPackage(
+    {},
+    ['@pnpm.e2e/bravo'],
+    testDefaults({ resolutionMode: 'time-based' })
+  )
+
+  const lockfile = project.readLockfile()
+  expect(lockfile.packages['@pnpm.e2e/bravo-dep@1.0.1']).toBeTruthy()
+  await install(
+    {
+      dependencies: {
+        '@pnpm.e2e/bravo-dep': '^1.0.0',
+      },
+    },
+    testDefaults({ resolutionMode: 'lowest-direct' })
+  )
+
+  {
+    const lockfile = project.readLockfile()
+    expect(lockfile.packages['@pnpm.e2e/bravo-dep@1.0.0']).toBeTruthy()
+  }
+
+  await install({
+    dependencies: {
+      '@pnpm.e2e/bravo-dep': '^1.1.0',
+    },
+  }, testDefaults({ resolutionMode: 'lowest-direct' }))
+
+  {
+    const lockfile = project.readLockfile()
+    expect(lockfile.packages['@pnpm.e2e/bravo-dep@1.1.0']).toBeTruthy()
+  }
+})
diff --git a/resolving/npm-resolver/src/pickPackageFromMeta.ts b/resolving/npm-resolver/src/pickPackageFromMeta.ts
index 6e3497e19cf..87981188de5 100644
--- a/resolving/npm-resolver/src/pickPackageFromMeta.ts
+++ b/resolving/npm-resolver/src/pickPackageFromMeta.ts
@@ -91,7 +91,16 @@ export function pickLowestVersionByVersionRange (
   preferredVerSels?: VersionSelectors
 ) {
   if (preferredVerSels != null && Object.keys(preferredVerSels).length > 0) {
-    const prioritizedPreferredVersions = prioritizePreferredVersions(meta, versionRange, preferredVerSels)
+    // ignore the subdependencies
+    // {'^1.0.0': { selectorType: 'range', weight: 1000 }, '1.0.1': 'version'} would be [1.0.1, 1.0.0] if sorted by weight
+    let lowestPreferredVerSels: VersionSelectors | null = null
+    Object.entries(preferredVerSels).forEach(([key, value]) => {
+      if (value !== null && typeof value === 'object') {
+        if (!lowestPreferredVerSels) lowestPreferredVerSels = {}
+        lowestPreferredVerSels[key] = value
+      }
+    })
+    const prioritizedPreferredVersions = prioritizePreferredVersions(meta, versionRange, lowestPreferredVerSels ?? preferredVerSels)
     for (const preferredVersions of prioritizedPreferredVersions) {
       const preferredVersion = semver.minSatisfying(preferredVersions, versionRange, true)
       if (preferredVersion) {