diff --git a/nixosModules/clanCore/vars/default.nix b/nixosModules/clanCore/vars/default.nix
index 0fa5c6165..afe8962ad 100644
--- a/nixosModules/clanCore/vars/default.nix
+++ b/nixosModules/clanCore/vars/default.nix
@@ -40,6 +40,18 @@ in
   };
 
   config = {
+    # Check for removed passBackend option usage
+    assertions = [
+      {
+        assertion = config.clan.core.vars.settings.passBackend == null;
+        message = ''
+          The option `clan.core.vars.settings.passBackend' has been removed.
+          Use clan.vars.password-store.passPackage instead.
+          Set it to pkgs.pass for GPG or pkgs.passage for age encryption.
+        '';
+      }
+    ];
+
     # check all that all non-secret files have no owner/group/mode set
     warnings = lib.foldl' (
       warnings: generator:
diff --git a/nixosModules/clanCore/vars/secret/password-store.nix b/nixosModules/clanCore/vars/secret/password-store.nix
index 8b02be38d..d79c46cf4 100644
--- a/nixosModules/clanCore/vars/secret/password-store.nix
+++ b/nixosModules/clanCore/vars/secret/password-store.nix
@@ -62,6 +62,13 @@ in
         location where the tarball with the password-store secrets will be uploaded to and the manifest
       '';
     };
+    passPackage = lib.mkOption {
+      type = lib.types.package;
+      default = pkgs.pass;
+      description = ''
+        Password store package to use. Can be pkgs.pass for GPG-based storage or pkgs.passage for age-based storage.
+      '';
+    };
   };
   config = {
     clan.core.vars.settings =
@@ -76,7 +83,7 @@ in
                 else if file.config.neededFor == "services" then
                   "/run/secrets/${file.config.generatorName}/${file.config.name}"
                 else if file.config.neededFor == "activation" then
-                  "${config.clan.password-store.secretLocation}/activation/${file.config.generatorName}/${file.config.name}"
+                  "${config.clan.vars.password-store.secretLocation}/activation/${file.config.generatorName}/${file.config.name}"
                 else if file.config.neededFor == "partitioning" then
                   "/run/partitioning-secrets/${file.config.generatorName}/${file.config.name}"
                 else
diff --git a/nixosModules/clanCore/vars/settings-opts.nix b/nixosModules/clanCore/vars/settings-opts.nix
index 276da4e9e..226888111 100644
--- a/nixosModules/clanCore/vars/settings-opts.nix
+++ b/nixosModules/clanCore/vars/settings-opts.nix
@@ -15,17 +15,6 @@
     '';
   };
 
-  passBackend = lib.mkOption {
-    type = lib.types.enum [
-      "passage"
-      "pass"
-    ];
-    default = "pass";
-    description = ''
-      password-store backend to use. Valid options are `pass` and `passage`
-    '';
-  };
-
   secretModule = lib.mkOption {
     type = lib.types.str;
     internal = true;
@@ -65,4 +54,15 @@
       the python import path to the public module
     '';
   };
+
+  # Legacy option that guides migration
+  passBackend = lib.mkOption {
+    type = lib.types.nullOr lib.types.str;
+    default = null;
+    visible = false;
+    description = ''
+      DEPRECATED: This option has been removed. Use clan.vars.password-store.passPackage instead.
+      Set it to pkgs.pass for GPG or pkgs.passage for age encryption.
+    '';
+  };
 }
diff --git a/pkgs/clan-cli/clan_cli/machines/update.py b/pkgs/clan-cli/clan_cli/machines/update.py
index e0f539446..75c543c8c 100644
--- a/pkgs/clan-cli/clan_cli/machines/update.py
+++ b/pkgs/clan-cli/clan_cli/machines/update.py
@@ -124,8 +124,6 @@ def update_command(args: argparse.Namespace) -> None:
                 f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.{{share,dependencies,migrateFact,prompts}}",
                 f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.generators.*.files.*.{{secret,deploy,owner,group,mode,neededFor}}",
                 f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.facts.secretUploadDirectory",
-                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.vars.password-store.secretLocation",
-                f"clanInternals.machines.{system}.{{{','.join(machine_names)}}}.config.clan.core.vars.settings.passBackend",
             ]
         )
 
diff --git a/pkgs/clan-cli/clan_cli/tests/test_vars.py b/pkgs/clan-cli/clan_cli/tests/test_vars.py
index 181b2a543..274dd38fc 100644
--- a/pkgs/clan-cli/clan_cli/tests/test_vars.py
+++ b/pkgs/clan-cli/clan_cli/tests/test_vars.py
@@ -403,6 +403,19 @@ def test_generate_secret_var_password_store(
     shutil.copytree(test_root / "data" / "password-store", password_store_dir)
     monkeypatch.setenv("PASSWORD_STORE_DIR", str(password_store_dir))
 
+    # Initialize password store as a git repository
+    import subprocess
+
+    subprocess.run(["git", "init"], cwd=password_store_dir, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"],
+        cwd=password_store_dir,
+        check=True,
+    )
+    subprocess.run(
+        ["git", "config", "user.name", "Test User"], cwd=password_store_dir, check=True
+    )
+
     machine = Machine(name="my_machine", flake=Flake(str(flake.path)))
     assert not check_vars(machine.name, machine.flake)
     cli.run(["vars", "generate", "--flake", str(flake.path), "my_machine"])
diff --git a/pkgs/clan-cli/clan_cli/vars/generate.py b/pkgs/clan-cli/clan_cli/vars/generate.py
index 925c97b1a..2d1ef9c08 100644
--- a/pkgs/clan-cli/clan_cli/vars/generate.py
+++ b/pkgs/clan-cli/clan_cli/vars/generate.py
@@ -82,11 +82,6 @@ class Generator:
             files = []
             gen_files = files_data.get(gen_name, {})
             for file_name, file_data in gen_files.items():
-                # Handle mode conversion properly
-                mode = file_data["mode"]
-                if isinstance(mode, str):
-                    mode = int(mode, 8)
-
                 var = Var(
                     id=f"{gen_name}/{file_name}",
                     name=file_name,
@@ -94,7 +89,9 @@ class Generator:
                     deploy=file_data["deploy"],
                     owner=file_data["owner"],
                     group=file_data["group"],
-                    mode=mode,
+                    mode=file_data["mode"]
+                    if isinstance(file_data["mode"], int)
+                    else int(file_data["mode"], 8),
                     needed_for=file_data["neededFor"],
                 )
                 files.append(var)
diff --git a/pkgs/clan-cli/clan_cli/vars/secret_modules/password_store.py b/pkgs/clan-cli/clan_cli/vars/secret_modules/password_store.py
index 98060a997..d23cf18a4 100644
--- a/pkgs/clan-cli/clan_cli/vars/secret_modules/password_store.py
+++ b/pkgs/clan-cli/clan_cli/vars/secret_modules/password_store.py
@@ -1,9 +1,7 @@
 import io
 import logging
-import os
 import tarfile
 from collections.abc import Iterable
-from itertools import chain
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -12,7 +10,6 @@ from clan_cli.vars._types import StoreBase
 from clan_cli.vars.generate import Generator, Var
 from clan_lib.cmd import CmdOut, Log, RunOpts, run
 from clan_lib.machines.machines import Machine
-from clan_lib.nix import nix_shell
 from clan_lib.ssh.remote import Remote
 
 log = logging.getLogger(__name__)
@@ -26,31 +23,64 @@ class SecretStore(StoreBase):
     def __init__(self, machine: Machine) -> None:
         self.machine = machine
         self.entry_prefix = "clan-vars"
+        self._store_dir: Path | None = None
 
     @property
     def store_name(self) -> str:
         return "password_store"
 
     @property
-    def _store_backend(self) -> str:
-        backend = self.machine.select("config.clan.core.vars.settings.passBackend")
-        return backend
+    def store_dir(self) -> Path:
+        """Get the password store directory, cached after first access."""
+        if self._store_dir is None:
+            result = self._run_pass(
+                "git", "rev-parse", "--show-toplevel", options=RunOpts(check=False)
+            )
+            if result.returncode != 0:
+                msg = "Password store must be a git repository"
+                raise ValueError(msg)
+            self._store_dir = Path(result.stdout.strip())
+        return self._store_dir
 
     @property
-    def _password_store_dir(self) -> Path:
-        if self._store_backend == "passage":
-            lookup = os.environ.get("PASSAGE_DIR")
-            default = Path.home() / ".passage/store"
-        else:
-            lookup = os.environ.get("PASSWORD_STORE_DIR")
-            default = Path.home() / ".password-store"
-        return Path(lookup) if lookup else default
+    def _pass_command(self) -> str:
+        out_path = self.machine.select(
+            "config.clan.vars.password-store.passPackage.outPath"
+        )
+        main_program = (
+            self.machine.select(
+                "config.clan.vars.password-store.passPackage.?meta.?mainProgram"
+            )
+            .get("meta", {})
+            .get("mainProgram")
+        )
+
+        if main_program:
+            binary_path = Path(out_path) / "bin" / main_program
+            if binary_path.exists():
+                return str(binary_path)
+
+        # Look for common password store binaries
+        bin_dir = Path(out_path) / "bin"
+        if bin_dir.exists():
+            for binary in ["pass", "passage"]:
+                binary_path = bin_dir / binary
+                if binary_path.exists():
+                    return str(binary_path)
+
+            # If only one binary exists, use it
+            binaries = [f for f in bin_dir.iterdir() if f.is_file()]
+            if len(binaries) == 1:
+                return str(binaries[0])
+
+        msg = "Could not find password store binary in package"
+        raise ValueError(msg)
 
     def entry_dir(self, generator: Generator, name: str) -> Path:
         return Path(self.entry_prefix) / self.rel_dir(generator, name)
 
     def _run_pass(self, *args: str, options: RunOpts | None = None) -> CmdOut:
-        cmd = nix_shell(packages=["pass"], cmd=[self._store_backend, *args])
+        cmd = [self._pass_command, *args]
         return run(cmd, options)
 
     def _set(
@@ -68,9 +98,11 @@ class SecretStore(StoreBase):
         return self._run_pass("show", pass_name).stdout.encode()
 
     def exists(self, generator: Generator, name: str) -> bool:
-        extension = "age" if self._store_backend == "passage" else "gpg"
-        filename = f"{self.entry_dir(generator, name)}.{extension}"
-        return (self._password_store_dir / filename).exists()
+        pass_name = str(self.entry_dir(generator, name))
+        # Check if the file exists with either .age or .gpg extension
+        age_file = self.store_dir / f"{pass_name}.age"
+        gpg_file = self.store_dir / f"{pass_name}.gpg"
+        return age_file.exists() or gpg_file.exists()
 
     def delete(self, generator: Generator, name: str) -> Iterable[Path]:
         pass_name = str(self.entry_dir(generator, name))
@@ -79,66 +111,31 @@ class SecretStore(StoreBase):
 
     def delete_store(self) -> Iterable[Path]:
         machine_dir = Path(self.entry_prefix) / "per-machine" / self.machine.name
-        if not (self._password_store_dir / machine_dir).exists():
-            # The directory may not exist if the machine
-            # has no vars, or they have been deleted already.
-            return []
-        pass_call = ["rm", "--force", "--recursive", str(machine_dir)]
-        self._run_pass(*pass_call, options=RunOpts(check=True))
+        # Check if the directory exists in the password store before trying to delete
+        result = self._run_pass("ls", str(machine_dir), options=RunOpts(check=False))
+        if result.returncode == 0:
+            self._run_pass(
+                "rm",
+                "--force",
+                "--recursive",
+                str(machine_dir),
+                options=RunOpts(check=True),
+            )
         return []
 
     def generate_hash(self) -> bytes:
-        hashes = []
-        hashes.append(
-            run(
-                nix_shell(
-                    ["git"],
-                    [
-                        "git",
-                        "-C",
-                        str(self._password_store_dir),
-                        "log",
-                        "-1",
-                        "--format=%H",
-                        self.entry_prefix,
-                    ],
-                ),
-                RunOpts(check=False),
-            )
-            .stdout.strip()
-            .encode()
+        result = self._run_pass(
+            "git",
+            "log",
+            "-1",
+            "--format=%H",
+            self.entry_prefix,
+            options=RunOpts(check=False),
         )
-        shared_dir = self._password_store_dir / self.entry_prefix / "shared"
-        machine_dir = (
-            self._password_store_dir
-            / self.entry_prefix
-            / "per-machine"
-            / self.machine.name
-        )
-        for symlink in chain(shared_dir.glob("**/*"), machine_dir.glob("**/*")):
-            if symlink.is_symlink():
-                hashes.append(
-                    run(
-                        nix_shell(
-                            ["git"],
-                            [
-                                "git",
-                                "-C",
-                                str(self._password_store_dir),
-                                "log",
-                                "-1",
-                                "--format=%H",
-                                str(symlink),
-                            ],
-                        ),
-                        RunOpts(check=False),
-                    )
-                    .stdout.strip()
-                    .encode()
-                )
+        git_hash = result.stdout.strip().encode()
 
-        # we sort the hashes to make sure that the order is always the same
-        hashes.sort()
+        if not git_hash:
+            return b""
 
         from clan_cli.vars.generate import Generator
 
@@ -149,22 +146,24 @@ class SecretStore(StoreBase):
         for generator in generators:
             for file in generator.files:
                 manifest.append(f"{generator.name}/{file.name}".encode())
-        manifest += hashes
+
+        manifest.append(git_hash)
         return b"\n".join(manifest)
 
     def needs_upload(self, host: Remote) -> bool:
         local_hash = self.generate_hash()
+        if not local_hash:
+            return True
+
         remote_hash = host.run(
-            # TODO get the path to the secrets from the machine
             [
                 "cat",
-                f"{self.machine.select('config.clan.vars.password-store.secretLocation')}/.{self._store_backend}_info",
+                f"{self.machine.select('config.clan.vars.password-store.secretLocation')}/.pass_info",
             ],
             RunOpts(log=Log.STDERR, check=False),
         ).stdout.strip()
 
         if not remote_hash:
-            print("remote hash is empty")
             return True
 
         return local_hash.decode() != remote_hash
@@ -233,7 +232,9 @@ class SecretStore(StoreBase):
                         out_file.parent.mkdir(parents=True, exist_ok=True)
                         out_file.write_bytes(self.get(generator, file.name))
 
-        (output_dir / f".{self._store_backend}_info").write_bytes(self.generate_hash())
+        hash_data = self.generate_hash()
+        if hash_data:
+            (output_dir / ".pass_info").write_bytes(hash_data)
 
     def upload(self, host: Remote, phases: list[str]) -> None:
         if "partitioning" in phases:
diff --git a/pkgs/clan-cli/default.nix b/pkgs/clan-cli/default.nix
index 1e04822c7..be9dd935a 100644
--- a/pkgs/clan-cli/default.nix
+++ b/pkgs/clan-cli/default.nix
@@ -2,6 +2,7 @@
   # callPackage args
   gnupg,
   installShellFiles,
+  pass,
   jq,
   lib,
   nix,
@@ -58,6 +59,7 @@ let
 
   testDependencies = testRuntimeDependencies ++ [
     gnupg
+    pass
     stdenv.cc # Compiler used for certain native extensions
     (pythonRuntime.withPackages pyTestDeps)
   ];
@@ -213,6 +215,7 @@ pythonRuntime.pkgs.buildPythonApplication {
                 pkgs.shellcheck-minimal
                 pkgs.mkpasswd
                 pkgs.xkcdpass
+                pkgs.pass
                 nix-select
               ];
             };