diff --git a/module_auto_update/models/module.py b/module_auto_update/models/module.py
index 97b9325df4e..0789d01b9f2 100644
--- a/module_auto_update/models/module.py
+++ b/module_auto_update/models/module.py
@@ -45,6 +45,12 @@ def ensure_module_state(env, modules, state):
 class Module(models.Model):
     _inherit = "ir.module.module"
 
+    def _module_exists_on_disk(self):
+        """Check if the module has a directory on the filesystem."""
+        self.ensure_one()
+        module_path = get_module_path(self.name)
+        return bool(module_path and os.path.isdir(module_path))
+
     def _get_checksum_dir(self):
         self.ensure_one()
 
@@ -84,6 +90,8 @@ def _save_installed_checksums(self):
         checksums = {}
         installed_modules = self.search([("state", "=", "installed")])
         for module in installed_modules:
+            if not module._module_exists_on_disk():
+                continue
             checksums[module.name] = module._get_checksum_dir()
         self._save_checksums(checksums)
 
@@ -96,7 +104,8 @@ def _get_modules_with_changed_checksum(self):
         saved_checksums = self._get_saved_checksums()
         installed_modules = self.search([("state", "=", "installed")])
         return installed_modules.filtered(
-            lambda r: r._get_checksum_dir() != saved_checksums.get(r.name),
+            lambda r: r._module_exists_on_disk()
+            and r._get_checksum_dir() != saved_checksums.get(r.name),
         )
 
     @api.model
diff --git a/module_auto_update/tests/test_module.py b/module_auto_update/tests/test_module.py
index 6929b3cae53..a6233b20c13 100644
--- a/module_auto_update/tests/test_module.py
+++ b/module_auto_update/tests/test_module.py
@@ -80,6 +80,23 @@ def test_get_modules_with_changed_checksum(self):
         Imm._save_installed_checksums()
         self.assertFalse(Imm._get_modules_with_changed_checksum())
 
+    def test_get_modules_with_changed_checksum_skips_db_only_modules(self):
+        """Skip modules that exist only in DB (no filesystem path)."""
+        Imm = self.env["ir.module.module"]
+        base_module = Imm.search([("name", "=", "base")])
+        # Mock _module_exists_on_disk to simulate a diskless module
+        with mock.patch.object(
+            type(base_module), "_module_exists_on_disk", return_value=False
+        ):
+            self.assertFalse(base_module._module_exists_on_disk())
+            # Save checksums — base should be skipped
+            Imm._save_installed_checksums()
+            saved_checksums = Imm._get_saved_checksums()
+            self.assertNotIn("base", saved_checksums)
+            # Changed checksum detection should not include it
+            changed = Imm._get_modules_with_changed_checksum()
+            self.assertNotIn(base_module, changed)
+
 
 @odoo.tests.tagged("post_install", "-at_install")
 class TestModuleAfterInstall(TransactionCase):