diff --git a/lib/modules/manager/nix/__fixtures__/flake.1.lock b/lib/modules/manager/nix/__fixtures__/flake.1.lock
new file mode 100644
index 00000000000000..5999137c97311a
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.1.lock
@@ -0,0 +1,7 @@
+{
+  "nodes": {
+    "root": {}
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/__fixtures__/flake.2.lock b/lib/modules/manager/nix/__fixtures__/flake.2.lock
new file mode 100644
index 00000000000000..8bbf80d08a6d05
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.2.lock
@@ -0,0 +1,27 @@
+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1720031269,
+        "narHash": "sha256-rwz8NJZV+387rnWpTYcXaRNvzUSnnF9aHONoJIYmiUQ=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "9f4128e00b0ae8ec65918efeba59db998750ead6",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/__fixtures__/flake.3.lock b/lib/modules/manager/nix/__fixtures__/flake.3.lock
new file mode 100644
index 00000000000000..4e715e4b122a14
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.3.lock
@@ -0,0 +1,26 @@
+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1728650607,
+        "narHash": "sha256-0lOnVTzRXzpk5uxbHLm3Ti3tyPAvirAIQDfwEUd8arg=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "612ee628421ba2c1abca4c99684862f76cb3b089",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/__fixtures__/flake.4.lock b/lib/modules/manager/nix/__fixtures__/flake.4.lock
new file mode 100644
index 00000000000000..a11067f50b38fd
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.4.lock
@@ -0,0 +1,44 @@
+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1672057183,
+        "narHash": "sha256-GN7/10DNNvs1FPj9tlZA2qgNdFuYKKuS3qlHTqAxasQ=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "b139e44d78c36c69bcbb825b20dbfa51e7738347",
+        "type": "github"
+      },
+      "original": {
+        "id": "nixpkgs",
+        "ref": "nixpkgs-unstable",
+        "type": "indirect"
+      }
+    },
+    "patchelf": {
+      "inputs": {
+        "nixpkgs": "nixpkgs"
+      },
+      "locked": {
+        "lastModified": 1718457448,
+        "narHash": "sha256-FSoxTcRZMGHNJh8dNtKOkcUtjhmhU6yQXcZZfUPLhQM=",
+        "ref": "refs/heads/master",
+        "rev": "a0f54334df36770b335c051e540ba40afcbf8378",
+        "revCount": 844,
+        "type": "git",
+        "url": "https://github.com/NixOS/patchelf.git"
+      },
+      "original": {
+        "type": "git",
+        "url": "https://github.com/NixOS/patchelf.git"
+      }
+    },
+    "root": {
+      "inputs": {
+        "patchelf": "patchelf"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/__fixtures__/flake.5.lock b/lib/modules/manager/nix/__fixtures__/flake.5.lock
new file mode 100644
index 00000000000000..9e6349fa1f1baa
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.5.lock
@@ -0,0 +1,27 @@
+{
+  "nodes": {
+    "ijq": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1723569650,
+        "narHash": "sha256-Ho/sAhEUeSug52JALgjrKVUPCBe8+PovbJj/lniKxp8=",
+        "owner": "~gpanders",
+        "repo": "ijq",
+        "rev": "88f0d9ae98942bf49cba302c42b2a0f6e05f9b58",
+        "type": "sourcehut"
+      },
+      "original": {
+        "owner": "~gpanders",
+        "repo": "ijq",
+        "type": "sourcehut"
+      }
+    },
+    "root": {
+      "inputs": {
+        "ijq": "ijq"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/__fixtures__/flake.6.lock b/lib/modules/manager/nix/__fixtures__/flake.6.lock
new file mode 100644
index 00000000000000..3b4e21a8331a78
--- /dev/null
+++ b/lib/modules/manager/nix/__fixtures__/flake.6.lock
@@ -0,0 +1,27 @@
+{
+  "nodes": {
+    "home-manager": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1728650932,
+        "narHash": "sha256-mGKzqdsRyLnGNl6WjEr7+sghGgBtYHhJQ4mjpgRTCsU=",
+        "owner": "rycee",
+        "repo": "home-manager",
+        "rev": "65ae9c147349829d3df0222151f53f79821c5134",
+        "type": "gitlab"
+      },
+      "original": {
+        "owner": "rycee",
+        "repo": "home-manager",
+        "type": "gitlab"
+      }
+    },
+    "root": {
+      "inputs": {
+        "home-manager": "home-manager"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}
diff --git a/lib/modules/manager/nix/artifacts.spec.ts b/lib/modules/manager/nix/artifacts.spec.ts
index 7b741ee82208f4..d9cca2268fdde9 100644
--- a/lib/modules/manager/nix/artifacts.spec.ts
+++ b/lib/modules/manager/nix/artifacts.spec.ts
@@ -36,17 +36,14 @@ process.env.CONTAINERBASE = 'true';
 const config: UpdateArtifactsConfig = {};
 const lockMaintenanceConfig = { ...config, isLockFileMaintenance: true };
 const updateInputCmd = `nix \
-    --extra-experimental-features nix-command \
-    --extra-experimental-features flakes \
+--extra-experimental-features 'nix-command flakes' \
 flake lock --update-input nixpkgs`;
 const updateInputTokenCmd = `nix \
-    --extra-experimental-features nix-command \
-    --extra-experimental-features flakes \
+--extra-experimental-features 'nix-command flakes' \
 --extra-access-tokens github.com=token \
 flake lock --update-input nixpkgs`;
 const lockfileMaintenanceCmd = `nix \
-    --extra-experimental-features nix-command \
-    --extra-experimental-features flakes \
+--extra-experimental-features 'nix-command flakes' \
 flake update`;
 
 describe('modules/manager/nix/artifacts', () => {
@@ -66,7 +63,7 @@ describe('modules/manager/nix/artifacts', () => {
   it('returns if no flake.lock found', async () => {
     const execSnapshots = mockExecAll();
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [],
       newPackageFileContent: '',
       config,
@@ -86,7 +83,7 @@ describe('modules/manager/nix/artifacts', () => {
     );
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: 'some new content',
       config,
@@ -107,7 +104,7 @@ describe('modules/manager/nix/artifacts', () => {
     fs.readLocalFile.mockResolvedValueOnce('new flake.lock');
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: 'some new content',
       config: { ...config, constraints: { python: '3.7' } },
@@ -137,7 +134,7 @@ describe('modules/manager/nix/artifacts', () => {
     hostRules.find.mockReturnValueOnce({ token: 'token' });
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: 'some new content',
       config: { ...config, constraints: { python: '3.7' } },
@@ -167,7 +164,7 @@ describe('modules/manager/nix/artifacts', () => {
     hostRules.find.mockReturnValueOnce({ token: 'x-access-token:token' });
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: 'some new content',
       config: { ...config, constraints: { python: '3.7' } },
@@ -196,7 +193,7 @@ describe('modules/manager/nix/artifacts', () => {
     fs.readLocalFile.mockResolvedValueOnce('new flake.lock');
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: '{}',
       config: { ...config, constraints: { nix: '2.10.0' } },
@@ -241,7 +238,7 @@ describe('modules/manager/nix/artifacts', () => {
     fs.readLocalFile.mockResolvedValueOnce('new flake.lock');
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: '{}',
       config: { ...config, constraints: { nix: '2.10.0' } },
@@ -269,7 +266,7 @@ describe('modules/manager/nix/artifacts', () => {
     const execSnapshots = mockExecSequence([new Error('exec error')]);
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: '{}',
       config,
@@ -294,7 +291,7 @@ describe('modules/manager/nix/artifacts', () => {
     fs.readLocalFile.mockResolvedValueOnce('new flake.lock');
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: '{}',
       config: lockMaintenanceConfig,
@@ -323,7 +320,7 @@ describe('modules/manager/nix/artifacts', () => {
     fs.readLocalFile.mockResolvedValueOnce('new lock');
 
     const res = await updateArtifacts({
-      packageFileName: 'flake.nix',
+      packageFileName: 'flake.lock',
       updatedDeps: [{ depName: 'nixpkgs' }],
       newPackageFileContent: 'some new content',
       config: {
diff --git a/lib/modules/manager/nix/artifacts.ts b/lib/modules/manager/nix/artifacts.ts
index 411cfb160d6f97..4180f37bbc6f35 100644
--- a/lib/modules/manager/nix/artifacts.ts
+++ b/lib/modules/manager/nix/artifacts.ts
@@ -22,9 +22,7 @@ export async function updateArtifacts({
     return null;
   }
 
-  let cmd = `nix \
-    --extra-experimental-features nix-command \
-    --extra-experimental-features flakes `;
+  let cmd = `nix --extra-experimental-features 'nix-command flakes' `;
 
   const token = findGithubToken(
     hostRules.find({
diff --git a/lib/modules/manager/nix/extract.spec.ts b/lib/modules/manager/nix/extract.spec.ts
index 9645744c2a9208..b43320f7692dc4 100644
--- a/lib/modules/manager/nix/extract.spec.ts
+++ b/lib/modules/manager/nix/extract.spec.ts
@@ -1,74 +1,89 @@
 import { GitRefsDatasource } from '../../datasource/git-refs';
-import { id as nixpkgsVersioning } from '../../versioning/nixpkgs';
+import { Fixtures } from '../../../../test/fixtures';
 import { extractPackageFile } from '.';
 
+const flake1Lock = Fixtures.get('flake.1.lock');
+const flake2Lock = Fixtures.get('flake.2.lock');
+const flake3Lock = Fixtures.get('flake.3.lock');
+const flake4Lock = Fixtures.get('flake.4.lock');
+const flake5Lock = Fixtures.get('flake.5.lock');
+const flake6Lock = Fixtures.get('flake.6.lock');
+
 describe('modules/manager/nix/extract', () => {
-  it('returns null when no nixpkgs', () => {
-    const content = `{
-  inputs = {};
-}`;
-    const res = extractPackageFile(content);
+  it('returns null when no inputs', () => {
+    const res = extractPackageFile(flake1Lock, 'flake.lock');
 
     expect(res).toBeNull();
   });
 
-  it('returns nixpkgs', () => {
-    const content = `{
-  inputs = {
-    nixpkgs.url = "github:nixos/nixpkgs/nixos-21.11";
-  };
-}`;
-
-    const res = extractPackageFile(content);
+  it('returns nixpkgs input', () => {
+    const res = extractPackageFile(flake2Lock, 'flake.lock');
 
     expect(res?.deps).toEqual([
       {
         depName: 'nixpkgs',
-        currentValue: 'nixos-21.11',
+        currentDigest: '9f4128e00b0ae8ec65918efeba59db998750ead6',
         datasource: GitRefsDatasource.id,
         packageName: 'https://github.com/NixOS/nixpkgs',
-        versioning: nixpkgsVersioning,
       },
     ]);
   });
 
-  it('is case insensitive', () => {
-    const content = `{
-  inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs/nixos-21.11";
-  };
-}`;
+  it('includes nixpkgs with no explicit ref', () => {
+    const res = extractPackageFile(flake3Lock, 'flake.lock');
 
-    const res = extractPackageFile(content);
+    expect(res).toMatchObject({
+      deps: [
+        {
+          currentDigest: '612ee628421ba2c1abca4c99684862f76cb3b089',
+          datasource: 'git-refs',
+          depName: 'nixpkgs',
+          packageName: 'https://github.com/NixOS/nixpkgs',
+        },
+      ],
+    });
+  });
 
-    expect(res?.deps).toEqual([
-      {
-        depName: 'nixpkgs',
-        currentValue: 'nixos-21.11',
-        datasource: GitRefsDatasource.id,
-        packageName: 'https://github.com/NixOS/nixpkgs',
-        versioning: nixpkgsVersioning,
-      },
-    ]);
+  it('includes patchelf from HEAD', () => {
+    const res = extractPackageFile(flake4Lock, 'flake.lock');
+
+    expect(res).toMatchObject({
+      deps: [
+        {
+          currentDigest: 'a0f54334df36770b335c051e540ba40afcbf8378',
+          datasource: 'git-refs',
+          depName: 'patchelf',
+          packageName: 'https://github.com/NixOS/patchelf.git',
+        },
+      ],
+    });
   });
 
-  it('includes nixpkgs with no explicit ref', () => {
-    const content = `{
-  inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs";
-  };
-}`;
+  it('includes ijq from sourcehut without a flake', () => {
+    const res = extractPackageFile(flake5Lock, 'flake.lock');
+
+    expect(res).toMatchObject({
+      deps: [
+        {
+          currentDigest: '88f0d9ae98942bf49cba302c42b2a0f6e05f9b58',
+          datasource: 'git-refs',
+          depName: 'ijq',
+          packageName: 'https://git.sr.ht/~gpanders/ijq',
+        },
+      ],
+    });
+  });
 
-    const res = extractPackageFile(content);
+  it('includes home-manager from gitlab', () => {
+    const res = extractPackageFile(flake6Lock, 'flake.lock');
 
     expect(res).toMatchObject({
       deps: [
         {
-          currentValue: undefined,
+          currentDigest: '65ae9c147349829d3df0222151f53f79821c5134',
           datasource: 'git-refs',
-          depName: 'nixpkgs',
-          packageName: 'https://github.com/NixOS/nixpkgs',
-          versioning: 'nixpkgs',
+          depName: 'home-manager',
+          packageName: 'https://gitlab.com/rycee/home-manager',
         },
       ],
     });
diff --git a/lib/modules/manager/nix/extract.ts b/lib/modules/manager/nix/extract.ts
index 5170e23a07dfe0..a046b72182ff9c 100644
--- a/lib/modules/manager/nix/extract.ts
+++ b/lib/modules/manager/nix/extract.ts
@@ -1,23 +1,90 @@
-import { regEx } from '../../../util/regex';
 import { GitRefsDatasource } from '../../datasource/git-refs';
+import { logger } from '../../../logger';
 import { id as nixpkgsVersioning } from '../../versioning/nixpkgs';
 import type { PackageDependency, PackageFileContent } from '../types';
+import { InputType, NixFlakeLock } from './types';
 
-const nixpkgsRegex = regEx(/"github:nixos\/nixpkgs(\/(?<ref>[a-z0-9-.]+))?"/i);
+// TODO: add support to update nixpkgs branches in flakes.nix using nixpkgsVersioning
+
+export function extractPackageFile(
+  content: string,
+  packageFile: string,
+): PackageFileContent | null {
+  logger.trace(`nix.extractPackageFile(${packageFile})`);
 
-export function extractPackageFile(content: string): PackageFileContent | null {
   const deps: PackageDependency[] = [];
+  let lock: NixFlakeLock;
+
+  try {
+    lock = JSON.parse(content);
+  } catch {
+    logger.debug({ packageFile }, `Invalid JSON`);
+    return null;
+  }
+
+  if (lock.version !== 7) {
+    logger.debug({ packageFile }, 'Unsupported flake lock version');
+    return null;
+  }
+
+  for (const depName of Object.keys(lock.nodes ?? {})) {
+    // the root input is a magic string for the entrypoint and only references other flake inputs
+    if (depName === 'root') {
+      continue;
+    }
+
+    const flakeInput = lock.nodes[depName];
+    const flakeLocked = flakeInput.locked;
+    const flakeOriginal = flakeInput.original;
+
+    if (flakeLocked === undefined || flakeOriginal === undefined) {
+      logger.debug(
+        { packageFile },
+        `Found empty flake input '${JSON.stringify(flakeInput)}', skipping`,
+      );
+      continue;
+    }
+
+    // indirect inputs cannot be updated via normal means
+    if (flakeOriginal.type === InputType.indirect) {
+      continue;
+    }
 
-  const match = nixpkgsRegex.exec(content);
-  if (match?.groups) {
-    const { ref } = match.groups;
-    deps.push({
-      depName: 'nixpkgs',
-      currentValue: ref,
-      datasource: GitRefsDatasource.id,
-      packageName: 'https://github.com/NixOS/nixpkgs',
-      versioning: nixpkgsVersioning,
-    });
+    if (flakeLocked.type === InputType.github) {
+      deps.push({
+        depName,
+        currentDigest: flakeLocked.rev,
+        datasource: GitRefsDatasource.id,
+        packageName: `https://github.com/${flakeOriginal.owner}/${flakeOriginal.repo}`,
+      });
+    } else if (flakeLocked.type === InputType.gitlab) {
+      deps.push({
+        depName,
+        currentDigest: flakeLocked.rev,
+        datasource: GitRefsDatasource.id,
+        packageName: `https://gitlab.com/${flakeOriginal.owner}/${flakeOriginal.repo}`,
+      });
+    } else if (flakeOriginal.type === InputType.git) {
+      deps.push({
+        depName,
+        currentDigest: flakeLocked.rev,
+        datasource: GitRefsDatasource.id,
+        packageName: flakeOriginal.url,
+      });
+    } else if (flakeLocked.type === InputType.sourcehut) {
+      deps.push({
+        depName,
+        currentDigest: flakeLocked.rev,
+        datasource: GitRefsDatasource.id,
+        packageName: `https://git.sr.ht/${flakeOriginal.owner}/${flakeOriginal.repo}`,
+      });
+    } else {
+      logger.debug(
+        { packageFile },
+        `Unknown flake.lock type "${flakeLocked.type}", skipping`,
+      );
+      continue;
+    }
   }
 
   if (deps.length) {
diff --git a/lib/modules/manager/nix/index.ts b/lib/modules/manager/nix/index.ts
index 7cdfa48cdeb1bd..9444bce8d06616 100644
--- a/lib/modules/manager/nix/index.ts
+++ b/lib/modules/manager/nix/index.ts
@@ -6,8 +6,8 @@ export { updateArtifacts } from './artifacts';
 export const supportsLockFileMaintenance = true;
 
 export const defaultConfig = {
-  fileMatch: ['(^|/)flake\\.nix$'],
-  commitMessageTopic: 'nixpkgs',
+  fileMatch: ['(^|/)flake\\.lock'],
+  commitMessageTopic: 'nix',
   commitMessageExtra: 'to {{newValue}}',
   enabled: false,
 };
diff --git a/lib/modules/manager/nix/readme.md b/lib/modules/manager/nix/readme.md
index 3a196a34445c0e..c1357a8519bd20 100644
--- a/lib/modules/manager/nix/readme.md
+++ b/lib/modules/manager/nix/readme.md
@@ -1,4 +1,4 @@
 The [`nix`](https://github.com/NixOS/nix) manager supports:
 
 - [`lockFileMaintenance`](../../../configuration-options.md#lockfilemaintenance) updates for `flake.lock`
-- [nixpkgs](https://github.com/NixOS/nixpkgs) updates
+- input updates for `flake.lock`
diff --git a/lib/modules/manager/nix/types.ts b/lib/modules/manager/nix/types.ts
new file mode 100644
index 00000000000000..c0d65791e4ce7e
--- /dev/null
+++ b/lib/modules/manager/nix/types.ts
@@ -0,0 +1,39 @@
+export interface NixFlakeLock {
+  readonly nodes: Record<string, NixInput>;
+  readonly root: string;
+  readonly version: number;
+}
+
+export interface NixInput {
+  readonly inputs?: Record<string, string>;
+  readonly locked?: LockedInput;
+  readonly original?: OriginalInput;
+}
+
+export interface LockedInput {
+  readonly lastModified: number;
+  readonly narHash: string;
+  readonly owner?: string;
+  readonly repo?: string;
+  readonly ref?: string;
+  readonly rev: string;
+  readonly revCount: number;
+  readonly type: InputType;
+  readonly url?: string;
+}
+
+export interface OriginalInput {
+  readonly owner?: string;
+  readonly repo?: string;
+  readonly ref?: string;
+  readonly type: InputType;
+  readonly url?: string;
+}
+
+export enum InputType {
+  git = 'git',
+  github = 'github',
+  gitlab = 'gitlab',
+  indirect = 'indirect',
+  sourcehut = 'sourcehut',
+}