diff --git a/lib/crates/fabro-api/src/server.rs b/lib/crates/fabro-api/src/server.rs
index 111f0e546..5f1ac01fe 100644
--- a/lib/crates/fabro-api/src/server.rs
+++ b/lib/crates/fabro-api/src/server.rs
@@ -529,6 +529,7 @@ async fn start_run(
         }),
         ..Default::default()
     };
+    let run_labels = config.labels.clone();
     let persisted = match operations::create(
         &req.dot_source,
         RunCreateOptions {
@@ -536,7 +537,7 @@ async fn start_run(
             run_dir: Some(run_dir.clone()),
             run_id: Some(run_id.clone()),
             workflow_slug: None,
-            labels: std::collections::HashMap::new(),
+            labels: run_labels,
             base_branch: None,
             working_directory: Some(
                 std::env::current_dir().unwrap_or_else(|_| std::path::PathBuf::from(".")),
diff --git a/lib/crates/fabro-cli/src/commands/run/create.rs b/lib/crates/fabro-cli/src/commands/run/create.rs
index fa3b4c427..ac57babfe 100644
--- a/lib/crates/fabro-cli/src/commands/run/create.rs
+++ b/lib/crates/fabro-cli/src/commands/run/create.rs
@@ -76,7 +76,11 @@ pub async fn create_run(
             run_dir: Some(run_dir.clone()),
             run_id: Some(run_id.clone()),
             workflow_slug: source_input.workflow_slug.clone(),
-            labels: parse_labels(&args.label),
+            labels: {
+                let mut labels = source_input.config.labels.clone();
+                labels.extend(parse_labels(&args.label));
+                labels
+            },
             base_branch,
             working_directory: Some(working_directory.clone()),
             host_repo_path: Some(working_directory.to_string_lossy().to_string()),
diff --git a/lib/crates/fabro-cli/src/commands/run/execute.rs b/lib/crates/fabro-cli/src/commands/run/execute.rs
index a59f41bb5..1cca9ab33 100644
--- a/lib/crates/fabro-cli/src/commands/run/execute.rs
+++ b/lib/crates/fabro-cli/src/commands/run/execute.rs
@@ -528,7 +528,12 @@ pub(crate) fn load_workflow_source_input(
 
     let raw_source = read_workflow_file(&dot_path)?;
     let cli_goal = resolve_cli_goal(goal, goal_file)?;
-    let goal_override = cli_goal.or_else(|| config.goal.clone());
+    let goal_override = cli_goal.or_else(|| config.goal.clone()).or_else(|| {
+        config
+            .goal_file
+            .as_ref()
+            .and_then(|path| resolve_cli_goal(None, Some(path)).ok().flatten())
+    });
 
     let workflow_toml_path = if resolved_workflow_path
         .extension()
@@ -847,7 +852,11 @@ async fn run_command_impl(
                     run_dir: Some(run_dir.clone()),
                     run_id: Some(run_id.clone()),
                     workflow_slug: source_input.workflow_slug.clone(),
-                    labels: parse_labels(&label_vec),
+                    labels: {
+                        let mut labels = source_input.config.labels.clone();
+                        labels.extend(parse_labels(&label_vec));
+                        labels
+                    },
                     base_branch: detected_base_branch.clone(),
                     working_directory: Some(original_cwd.clone()),
                     host_repo_path: Some(original_cwd.to_string_lossy().to_string()),
diff --git a/lib/crates/fabro-config/src/config.rs b/lib/crates/fabro-config/src/config.rs
index 63e03e945..3c376bc26 100644
--- a/lib/crates/fabro-config/src/config.rs
+++ b/lib/crates/fabro-config/src/config.rs
@@ -31,9 +31,15 @@ pub struct FabroConfig {
     #[serde(default, skip_serializing_if = "Option::is_none")]
     pub goal: Option<String>,
 
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub goal_file: Option<PathBuf>,
+
     #[serde(default, skip_serializing_if = "Option::is_none")]
     pub graph: Option<String>,
 
+    #[serde(default, skip_serializing_if = "HashMap::is_empty")]
+    pub labels: HashMap<String, String>,
+
     // --- Run defaults fields (inlined) ---
     #[serde(default, alias = "directory", skip_serializing_if = "Option::is_none")]
     pub work_dir: Option<String>,
@@ -178,9 +184,17 @@ impl FabroConfig {
         if overlay.goal.is_some() {
             self.goal = overlay.goal;
         }
+        if overlay.goal_file.is_some() {
+            self.goal_file = overlay.goal_file;
+        }
         if overlay.graph.is_some() {
             self.graph = overlay.graph;
         }
+        if !overlay.labels.is_empty() {
+            let mut merged = std::mem::take(&mut self.labels);
+            merged.extend(overlay.labels);
+            self.labels = merged;
+        }
 
         // --- Run defaults fields ---
         if overlay.work_dir.is_some() {