diff --git a/metaflow/metaflow_config.py b/metaflow/metaflow_config.py
index bb42e0f5e3c..a1063f7e8d3 100644
--- a/metaflow/metaflow_config.py
+++ b/metaflow/metaflow_config.py
@@ -546,7 +546,7 @@
 # Feature flag (experimental features that are *explicitly* unsupported)
 
 # Process configs even when using the click_api for Runner/Deployer
-CLICK_API_PROCESS_CONFIG = from_conf("CLICK_API_PROCESS_CONFIG", False)
+CLICK_API_PROCESS_CONFIG = from_conf("CLICK_API_PROCESS_CONFIG", True)
 
 
 # PINNED_CONDA_LIBS are the libraries that metaflow depends on for execution
diff --git a/metaflow/runner/click_api.py b/metaflow/runner/click_api.py
index bda7ddb0157..e86d7b0a0ad 100644
--- a/metaflow/runner/click_api.py
+++ b/metaflow/runner/click_api.py
@@ -474,11 +474,22 @@ def _compute_flow_parameters(self):
 
                 ds = opts.get("datastore", defaults["datastore"])
                 quiet = opts.get("quiet", defaults["quiet"])
+
+                # Check for environment variables first
+
                 is_default = False
                 config_file = opts.get("config")
                 if config_file is None:
-                    is_default = True
-                    config_file = defaults.get("config")
+                    # Check if it was set through an environment variable -- we
+                    # don't have click process them here so we need to "fake" it.
+                    env_config_file = os.environ.get("METAFLOW_FLOW_CONFIG")
+                    if env_config_file:
+                        # Convert dict items to list of tuples
+                        config_file = list(json.loads(env_config_file).items())
+                        is_default = False
+                    else:
+                        is_default = True
+                        config_file = defaults.get("config")
 
                 if config_file:
                     config_file = dict(
@@ -494,8 +505,19 @@ def _compute_flow_parameters(self):
                 is_default = False
                 config_value = opts.get("config-value")
                 if config_value is None:
-                    is_default = True
-                    config_value = defaults.get("config_value")
+                    env_config_value = os.environ.get("METAFLOW_FLOW_CONFIG_VALUE")
+                    if env_config_value:
+                        # Parse environment variable using MultipleTuple logic
+                        loaded = json.loads(env_config_value)
+                        # Convert dict items to list of tuples with JSON-serialized values
+                        config_value = [
+                            (k, json.dumps(v) if not isinstance(v, str) else v)
+                            for k, v in loaded.items()
+                        ]
+                        is_default = False
+                    else:
+                        is_default = True
+                        config_value = defaults.get("config_value")
 
                 if config_value:
                     config_value = dict(