diff --git a/lib/modules/manager/nix/__fixtures__/flake.8.lock b/lib/modules/manager/nix/__fixtures__/flake.8.lock
new file mode 100644
index 00000000000000..ae61fdc2725739
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.8.lock
@@ -0,0 +1,28 @@
+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1728492678,
+        "narHash": "sha256-9UTxR8eukdg+XZeHgxW5hQA9fIKHsKCdOIUycTryeVw=",
+        "ref": "nixos-unstable",
+        "rev": "5633bcff0c6162b9e4b5f1264264611e950c8ec7",
+        "shallow": true,
+        "type": "git",
+        "url": "https://github.com/NixOS/nixpkgs"
+      },
+      "original": {
+        "ref": "nixos-unstable",
+        "shallow": true,
+        "type": "git",
+        "url": "https://github.com/NixOS/nixpkgs"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/extract.spec.ts b/lib/modules/manager/nix/extract.spec.ts
index e54ac96903e48e..8118d3bd8673e6 100644
--- a/lib/modules/manager/nix/extract.spec.ts
+++ b/lib/modules/manager/nix/extract.spec.ts
@@ -9,6 +9,7 @@ const flake4Lock = Fixtures.get('flake.4.lock');
 const flake5Lock = Fixtures.get('flake.5.lock');
 const flake6Lock = Fixtures.get('flake.6.lock');
 const flake7Lock = Fixtures.get('flake.7.lock');
+const flake8Lock = Fixtures.get('flake.8.lock');
 
 describe('modules/manager/nix/extract', () => {
   it('returns null when no inputs', () => {
@@ -75,4 +76,15 @@ describe('modules/manager/nix/extract', () => {
   it('test other version', () => {
     expect(extractPackageFile(flake7Lock, 'flake.lock')).toBeNull();
   });
+
+  it('includes nixpkgs with ref and shallow arguments', () => {
+    expect(extractPackageFile(flake8Lock, 'flake.lock')?.deps).toMatchObject([
+      {
+        currentDigest: '5633bcff0c6162b9e4b5f1264264611e950c8ec7',
+        datasource: 'git-refs',
+        depName: 'nixpkgs',
+        packageName: 'https://github.com/NixOS/nixpkgs',
+      },
+    ]);
+  });
 });
diff --git a/lib/modules/manager/nix/schema.ts b/lib/modules/manager/nix/schema.ts
index fabf2fa32fd066..559ee84c68a96e 100644
--- a/lib/modules/manager/nix/schema.ts
+++ b/lib/modules/manager/nix/schema.ts
@@ -18,6 +18,7 @@ export const LockedInput = z.object({
   ref: z.string().optional(),
   rev: z.string(),
   revCount: z.number().optional(),
+  shallow: z.boolean().optional(),
   type: InputType,
   url: z.string().optional(),
 });