diff --git a/docs/user_guide/config.md b/docs/user_guide/config.md
index bfc6e4da..27c53d67 100644
--- a/docs/user_guide/config.md
+++ b/docs/user_guide/config.md
@@ -4,8 +4,8 @@ The config module contains a mechanism to collect configuration parameters from
 It will load an (optional) provided config file, or alternatively use a passed python dictionary as initial config dictionary, and subsequently look for the following additional config files to load:
 
 * ``folder_config``: A config file of name :file:`sed_config.yaml` in the current working directory. This is mostly intended to pass calibration parameters of the workflow between different notebook instances.
-* ``user_config``: A config file provided by the user, stored as :file:`.sed/config.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
-* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config`
+* ``user_config``: A config file provided by the user, stored as :file:`.config/sed/config_v1.yaml` in the current user's home directly. This is intended to give a user the option for individual configuration modifications of system settings.
+* ``system_config``: A config file provided by the system administrator, stored as :file:`/etc/sed/config_v1.yaml` on Linux-based systems, and :file:`%ALLUSERSPROFILE%/sed/config_v1.yaml` on Windows. This should provide all necessary default parameters for using the sed processor with a given setup. For an example for an mpes setup, see :ref:`example_config`
 * ``default_config``: The default configuration shipped with the package. Typically, all parameters here should be overwritten by any of the other configuration files.
 
 The config mechanism returns the combined dictionary, and reports the loaded configuration files. In order to disable or overwrite any of the configuration files, they can be also given as optional parameters (path to a file, or python dictionary).
diff --git a/src/sed/core/config.py b/src/sed/core/config.py
index 686ee5b3..42f21153 100644
--- a/src/sed/core/config.py
+++ b/src/sed/core/config.py
@@ -19,6 +19,11 @@
 package_dir = os.path.dirname(find_spec("sed").origin)
 
 USER_CONFIG_PATH = user_config_path(appname="sed", appauthor="OpenCOMPES", ensure_exists=True)
+SYSTEM_CONFIG_PATH = (
+    Path(os.environ["ALLUSERSPROFILE"]).joinpath("sed")
+    if platform.system() == "Windows"
+    else Path("/etc/").joinpath("sed")
+)
 
 # Configure logging
 logger = setup_logging("config")
@@ -49,11 +54,11 @@ def parse_config(
         user_config (dict | str, optional): user-based config dictionary
             or file path. The loaded dictionary is completed with the user-based values,
             taking preference over system and default values.
-            Defaults to the file ".sed/config.yaml" in the current user's home directory.
+            Defaults to the file ".config/sed/config_v1.yaml" in the current user's home directory.
         system_config (dict | str, optional): system-wide config dictionary
             or file path. The loaded dictionary is completed with the system-wide values,
-            taking preference over default values. Defaults to the file "/etc/sed/config.yaml"
-            on linux, and "%ALLUSERSPROFILE%/sed/config.yaml" on windows.
+            taking preference over default values. Defaults to the file "/etc/sed/config_v1.yaml"
+            on linux, and "%ALLUSERSPROFILE%/sed/config_v1.yaml" on windows.
         default_config (dict | str, optional): default config dictionary
             or file path. The loaded dictionary is completed with the default values.
             Defaults to *package_dir*/config/default.yaml".
@@ -93,9 +98,7 @@ def parse_config(
         user_dict = copy.deepcopy(user_config)
     else:
         if user_config is None:
-            user_config = str(
-                Path.home().joinpath(".sed").joinpath("config.yaml"),
-            )
+            user_config = str(USER_CONFIG_PATH.joinpath("config_v1.yaml"))
         if Path(user_config).exists():
             user_dict = load_config(user_config)
             if verbose:
@@ -106,14 +109,7 @@ def parse_config(
         system_dict = copy.deepcopy(system_config)
     else:
         if system_config is None:
-            if platform.system() in ["Linux", "Darwin"]:
-                system_config = str(
-                    Path("/etc/").joinpath("sed").joinpath("config.yaml"),
-                )
-            elif platform.system() == "Windows":
-                system_config = str(
-                    Path(os.environ["ALLUSERSPROFILE"]).joinpath("sed").joinpath("config.yaml"),
-                )
+            system_config = str(SYSTEM_CONFIG_PATH.joinpath("config_v1.yaml"))
         if Path(system_config).exists():
             system_dict = load_config(system_config)
             if verbose:
@@ -281,6 +277,7 @@ def read_env_var(var_name: str) -> str | None:
     1. OS environment variables
     2. .env file in current directory
     3. .env file in user config directory
+    4. .env file in system config directory
 
     Args:
         var_name (str): Name of the environment variable to read
@@ -288,24 +285,30 @@ def read_env_var(var_name: str) -> str | None:
     Returns:
         str | None: Value of the environment variable or None if not found
     """
-    # First check OS environment variables
+    # 1. check OS environment variables
     value = os.getenv(var_name)
     if value is not None:
         logger.debug(f"Found {var_name} in OS environment variables")
         return value
 
-    # Then check .env in current directory
+    # 2. check .env in current directory
     local_vars = _parse_env_file(Path(".env"))
     if var_name in local_vars:
         logger.debug(f"Found {var_name} in ./.env file")
         return local_vars[var_name]
 
-    # Finally check .env in user config directory
+    # 3. check .env in user config directory
     user_vars = _parse_env_file(USER_CONFIG_PATH / ".env")
     if var_name in user_vars:
         logger.debug(f"Found {var_name} in user config .env file")
         return user_vars[var_name]
 
+    # 4. check .env in system config directory
+    system_vars = _parse_env_file(SYSTEM_CONFIG_PATH / ".env")
+    if var_name in system_vars:
+        logger.debug(f"Found {var_name} in system config .env file")
+        return system_vars[var_name]
+
     logger.debug(f"Environment variable {var_name} not found in any location")
     return None