diff --git a/pkgs/clan-cli/clan_cli/vars/set.py b/pkgs/clan-cli/clan_cli/vars/set.py
index 89681f0b7..b6f51337a 100644
--- a/pkgs/clan-cli/clan_cli/vars/set.py
+++ b/pkgs/clan-cli/clan_cli/vars/set.py
@@ -4,6 +4,7 @@ import sys
 
 from clan_cli.clan_uri import FlakeId
 from clan_cli.completions import add_dynamic_completer, complete_machines
+from clan_cli.git import commit_files
 from clan_cli.machines.machines import Machine
 from clan_cli.vars.get import get_var
 from clan_cli.vars.prompt import PromptType
@@ -25,7 +26,13 @@ def set_var(
         _var = get_var(_machine, var)
     else:
         _var = var
-    _var.set(value)
+    path = _var.set(value)
+    if path:
+        commit_files(
+            [path],
+            _machine.flake_dir,
+            f"Update var {_var.id} for machine {_machine.name}",
+        )
 
 
 def set_via_stdin(machine: str, var_id: str, flake: FlakeId) -> None:
diff --git a/pkgs/clan-cli/clan_cli/vars/var.py b/pkgs/clan-cli/clan_cli/vars/var.py
index 74324a406..f6030da53 100644
--- a/pkgs/clan-cli/clan_cli/vars/var.py
+++ b/pkgs/clan-cli/clan_cli/vars/var.py
@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
 if TYPE_CHECKING:
@@ -45,10 +46,10 @@ class Var:
         except UnicodeDecodeError:
             return "<binary blob>"
 
-    def set(self, value: bytes) -> None:
+    def set(self, value: bytes) -> Path | None:
         assert self._store is not None
         assert self._generator is not None
-        self._store.set(self._generator, self, value)
+        return self._store.set(self._generator, self, value)
 
     @property
     def exists(self) -> bool:
diff --git a/pkgs/clan-cli/tests/test_vars.py b/pkgs/clan-cli/tests/test_vars.py
index 966762aa9..517548c1a 100644
--- a/pkgs/clan-cli/tests/test_vars.py
+++ b/pkgs/clan-cli/tests/test_vars.py
@@ -766,6 +766,17 @@ def test_commit_message(
         commit_message
         == "Update vars via generator my_secret_generator for machine my_machine"
     )
+    # ensure `clan vars set` also sets a reasonable commit message
+    set_var(
+        "my_machine",
+        "my_generator/my_value",
+        b"world",
+        FlakeId(str(flake.path)),
+    )
+    commit_message = run(
+        ["git", "log", "-1", "--pretty=%B"],
+    ).stdout.strip()
+    assert all(x in commit_message for x in ["Update var", "my_generator", "my_value"])
 
 
 @pytest.mark.with_core