diff --git a/.changeset/clean-catalog-overrides.md b/.changeset/clean-catalog-overrides.md
new file mode 100644
index 0000000000..80439bb65b
--- /dev/null
+++ b/.changeset/clean-catalog-overrides.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/workspace.workspace-manifest-writer": patch
+"pnpm": patch
+---
+
+Prevent catalog entries from being removed by `cleanupUnusedCatalogs` when they are referenced only from workspace `overrides` in `pnpm-workspace.yaml`.
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 88477f736e..0527b5c036 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -9112,6 +9112,9 @@ importers:
       '@pnpm/catalogs.types':
         specifier: workspace:*
         version: link:../../catalogs/types
+      '@pnpm/config.parse-overrides':
+        specifier: workspace:*
+        version: link:../../config/parse-overrides
       '@pnpm/constants':
         specifier: workspace:*
         version: link:../../core/constants
diff --git a/workspace/workspace-manifest-writer/package.json b/workspace/workspace-manifest-writer/package.json
index 9901e50c41..1494b9b8c0 100644
--- a/workspace/workspace-manifest-writer/package.json
+++ b/workspace/workspace-manifest-writer/package.json
@@ -32,6 +32,7 @@
   },
   "dependencies": {
     "@pnpm/catalogs.types": "workspace:*",
+    "@pnpm/config.parse-overrides": "workspace:*",
     "@pnpm/constants": "workspace:*",
     "@pnpm/lockfile.types": "workspace:*",
     "@pnpm/object.key-sorting": "workspace:*",
diff --git a/workspace/workspace-manifest-writer/src/index.ts b/workspace/workspace-manifest-writer/src/index.ts
index 72389260b9..0b8297a6d3 100644
--- a/workspace/workspace-manifest-writer/src/index.ts
+++ b/workspace/workspace-manifest-writer/src/index.ts
@@ -3,6 +3,7 @@ import path from 'node:path'
 import util from 'node:util'
 
 import type { Catalogs } from '@pnpm/catalogs.types'
+import { parsePkgAndParentSelector } from '@pnpm/config.parse-overrides'
 import { type GLOBAL_CONFIG_YAML_FILENAME, WORKSPACE_MANIFEST_FILENAME } from '@pnpm/constants'
 import type { ResolvedCatalogEntry } from '@pnpm/lockfile.types'
 import { sortKeysByPriority } from '@pnpm/object.key-sorting'
@@ -168,14 +169,24 @@ function removePackagesFromWorkspaceCatalog (manifest: Partial<WorkspaceManifest
       if (!deps) continue
 
       for (const [pkgName, version] of Object.entries(deps)) {
-        if (!packageReferences[pkgName]) {
-          packageReferences[pkgName] = new Set()
-        }
-        packageReferences[pkgName].add(version)
+        addPackageReference(packageReferences, pkgName, version)
       }
     }
   }
 
+  for (const [selector, version] of Object.entries(manifest.overrides ?? {})) {
+    if (!version.startsWith('catalog:')) {
+      continue
+    }
+    let pkgName: string
+    try {
+      pkgName = parsePkgAndParentSelector(selector).targetPkg.name
+    } catch {
+      continue
+    }
+    addPackageReference(packageReferences, pkgName, version)
+  }
+
   if (manifest.catalog) {
     const packagesToRemove = Object.keys(manifest.catalog).filter(pkg =>
       !packageReferences[pkg]?.has('catalog:')
@@ -226,3 +237,10 @@ function removePackagesFromWorkspaceCatalog (manifest: Partial<WorkspaceManifest
 
   return shouldBeUpdated
 }
+
+function addPackageReference (packageReferences: Record<string, Set<string>>, pkgName: string, version: string): void {
+  if (!packageReferences[pkgName]) {
+    packageReferences[pkgName] = new Set()
+  }
+  packageReferences[pkgName].add(version)
+}
diff --git a/workspace/workspace-manifest-writer/test/removeCatalogs.test.ts b/workspace/workspace-manifest-writer/test/removeCatalogs.test.ts
index d381b2592b..7ed093f78c 100644
--- a/workspace/workspace-manifest-writer/test/removeCatalogs.test.ts
+++ b/workspace/workspace-manifest-writer/test/removeCatalogs.test.ts
@@ -415,3 +415,97 @@ test('when allProjects is undefined should not cleanup unused catalogs', async (
     },
   })
 })
+
+test('keep catalogs referenced only in workspace overrides', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFileSync(filePath, {
+    catalog: {
+      foo: '1.0.0',
+    },
+    catalogs: {
+      bar: {
+        '@scope/def': '2.0.0',
+      },
+    },
+    overrides: {
+      foo: 'catalog:',
+      '@scope/parent@1>@scope/def': 'catalog:bar',
+    },
+  })
+
+  prepare({
+    dependencies: {
+      zoo: '^1.0.0',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+
+  expect(readYamlFileSync(filePath)).toStrictEqual({
+    catalog: {
+      foo: '1.0.0',
+    },
+    catalogs: {
+      bar: {
+        '@scope/def': '2.0.0',
+      },
+    },
+    overrides: {
+      foo: 'catalog:',
+      '@scope/parent@1>@scope/def': 'catalog:bar',
+    },
+  })
+})
+
+test('remove catalogs unused by dependencies and workspace overrides', async () => {
+  const dir = tempDir(false)
+  const filePath = path.join(dir, WORKSPACE_MANIFEST_FILENAME)
+  writeYamlFileSync(filePath, {
+    catalog: {
+      foo: '1.0.0',
+      unusedDefault: '2.0.0',
+    },
+    catalogs: {
+      bar: {
+        def: '2.0.0',
+        unusedNamed: '3.0.0',
+      },
+    },
+    overrides: {
+      foo: 'catalog:',
+      def: 'catalog:bar',
+    },
+  })
+
+  prepare({
+    dependencies: {
+      zoo: '^1.0.0',
+    },
+  }, { tempDir: dir })
+  const allProjects = await findPackages(dir)
+
+  await updateWorkspaceManifest(dir, {
+    cleanupUnusedCatalogs: true,
+    allProjects,
+  })
+
+  expect(readYamlFileSync(filePath)).toStrictEqual({
+    catalog: {
+      foo: '1.0.0',
+    },
+    catalogs: {
+      bar: {
+        def: '2.0.0',
+      },
+    },
+    overrides: {
+      foo: 'catalog:',
+      def: 'catalog:bar',
+    },
+  })
+})
diff --git a/workspace/workspace-manifest-writer/tsconfig.json b/workspace/workspace-manifest-writer/tsconfig.json
index 415a296f3d..16fdff7018 100644
--- a/workspace/workspace-manifest-writer/tsconfig.json
+++ b/workspace/workspace-manifest-writer/tsconfig.json
@@ -18,6 +18,9 @@
     {
       "path": "../../catalogs/types"
     },
+    {
+      "path": "../../config/parse-overrides"
+    },
     {
       "path": "../../core/constants"
     },