diff --git a/providers/fab/src/airflow/providers/fab/auth_manager/cli_commands/utils.py b/providers/fab/src/airflow/providers/fab/auth_manager/cli_commands/utils.py
index 6d2ed506930f1..76fbb85776b9e 100644
--- a/providers/fab/src/airflow/providers/fab/auth_manager/cli_commands/utils.py
+++ b/providers/fab/src/airflow/providers/fab/auth_manager/cli_commands/utils.py
@@ -56,6 +56,7 @@ def get_application_builder() -> Generator[AirflowAppBuilder, None, None]:
     with flask_app.app_context():
         # Enable customizations in webserver_config.py to be applied via Flask.current_app.
         flask_app.config.from_pyfile(webserver_config, silent=True)
+        flask_app.config.from_prefixed_env(prefix="AIRFLOW__FAB__CONFIG__")
         flask_app.config["SQLALCHEMY_DATABASE_URI"] = conf.get("database", "SQL_ALCHEMY_CONN")
         url = make_url(flask_app.config["SQLALCHEMY_DATABASE_URI"])
         if url.drivername == "sqlite" and url.database and not isabs(url.database):
diff --git a/providers/fab/src/airflow/providers/fab/www/app.py b/providers/fab/src/airflow/providers/fab/www/app.py
index 57f21d95a4cbb..d5f092ba32bf7 100644
--- a/providers/fab/src/airflow/providers/fab/www/app.py
+++ b/providers/fab/src/airflow/providers/fab/www/app.py
@@ -70,6 +70,7 @@ def create_app(enable_plugins: bool):
     # Enable customizations in webserver_config.py to be applied via Flask.current_app.
     with flask_app.app_context():
         flask_app.config.from_pyfile(webserver_config, silent=True)
+        flask_app.config.from_prefixed_env(prefix="AIRFLOW__FAB__CONFIG__")
 
     url = make_url(flask_app.config["SQLALCHEMY_DATABASE_URI"])
     if url.drivername == "sqlite" and url.database and not isabs(url.database):
diff --git a/providers/fab/tests/unit/fab/auth_manager/cli_commands/test_utils.py b/providers/fab/tests/unit/fab/auth_manager/cli_commands/test_utils.py
index 633850e0df64d..0e9edf5a5864d 100644
--- a/providers/fab/tests/unit/fab/auth_manager/cli_commands/test_utils.py
+++ b/providers/fab/tests/unit/fab/auth_manager/cli_commands/test_utils.py
@@ -40,6 +40,7 @@ def flask_app():
 
         # Load webserver configuration
         flask_app.config.from_pyfile(webserver_config, silent=True)
+        flask_app.config.from_prefixed_env(prefix="AIRFLOW__FAB__CONFIG__")
 
         yield flask_app