diff --git a/src/mvt/common/config.py b/src/mvt/common/config.py
index ce29fb33..24bf4072 100644
--- a/src/mvt/common/config.py
+++ b/src/mvt/common/config.py
@@ -59,13 +59,16 @@ class MVTSettings(BaseSettings):
         dotenv_settings: PydanticBaseSettingsSource,
         file_secret_settings: PydanticBaseSettingsSource,
     ) -> Tuple[PydanticBaseSettingsSource, ...]:
-        yaml_source = YamlConfigSettingsSource(settings_cls, MVT_CONFIG_PATH)
         sources: Tuple[PydanticBaseSettingsSource, ...] = (
-            yaml_source,
+            YamlConfigSettingsSource(settings_cls, MVT_CONFIG_PATH),
             init_settings,
         )
-        # Always load env variables by default
-        sources = (env_settings,) + sources
+        # Load env variables only when asked to. initialise() constructs the
+        # settings once without them so that what gets written back to
+        # config.yaml never includes values taken from the environment.
+        # init_settings() returns the keyword arguments passed to the constructor.
+        if init_settings().get("load_env", True):
+            sources = (env_settings,) + sources
         return sources
 
     def save_settings(
@@ -92,7 +95,7 @@ class MVTSettings(BaseSettings):
 
         Afterwards we load the settings again, this time including the env variables.
         """
-        # Set invalid env prefix to avoid loading env variables.
+        # Construct the settings without env variables so they are not persisted.
         settings = cls(load_env=False)
         settings.save_settings()
 
diff --git a/tests/common/test_config.py b/tests/common/test_config.py
new file mode 100644
index 00000000..f471a583
--- /dev/null
+++ b/tests/common/test_config.py
@@ -0,0 +1,30 @@
+# Mobile Verification Toolkit (MVT)
+# Copyright (c) 2021-2026 The MVT Authors.
+# Use of this software is governed by the MVT License 1.1 that can be found at
+#   https://license.mvt.re/1.1/
+
+import os
+
+import yaml
+
+from mvt.common import config
+from mvt.common.config import MVTSettings
+
+
+def test_env_variables_are_not_persisted_to_config_file(tmp_path, monkeypatch):
+    config_path = tmp_path / "config.yaml"
+    monkeypatch.setattr(config, "MVT_CONFIG_FOLDER", str(tmp_path))
+    monkeypatch.setattr(config, "MVT_CONFIG_PATH", str(config_path))
+    monkeypatch.setenv("MVT_NETWORK_ACCESS_ALLOWED", "false")
+    monkeypatch.setenv("MVT_IOS_BACKUP_PASSWORD", "env-only-password")
+
+    settings = MVTSettings.initialise()
+
+    assert os.path.isfile(config_path)
+    saved = yaml.safe_load(config_path.read_text()) or {}
+    assert "NETWORK_ACCESS_ALLOWED" not in saved
+    assert "IOS_BACKUP_PASSWORD" not in saved
+
+    # The environment must still apply to the settings in use.
+    assert settings.NETWORK_ACCESS_ALLOWED is False
+    assert settings.IOS_BACKUP_PASSWORD == "env-only-password"