diff --git a/lib/crates/fabro-cli/src/manifest_builder.rs b/lib/crates/fabro-cli/src/manifest_builder.rs
index 716e77023..d88eb2599 100644
--- a/lib/crates/fabro-cli/src/manifest_builder.rs
+++ b/lib/crates/fabro-cli/src/manifest_builder.rs
@@ -660,4 +660,132 @@ mod tests {
                 .contains_key("fabro/workflows/child/workflow.fabro")
         );
     }
+
+    /// A relative `[run.goal] file = "..."` declared in `fabro.toml` must
+    /// resolve against the directory of `fabro.toml`, not against the
+    /// invocation cwd. We exercise this by invoking from a subdirectory
+    /// below the project root.
+    #[test]
+    #[allow(unsafe_code, clippy::allow_attributes)]
+    fn build_manifest_resolves_relative_goal_file_in_project_config() {
+        let temp = tempfile::tempdir().unwrap();
+        let project = temp.path();
+        let workflow_dir = project.join("fabro/workflows/demo");
+        std::fs::create_dir_all(&workflow_dir).unwrap();
+        std::fs::create_dir_all(project.join("prompts")).unwrap();
+
+        std::fs::write(
+            project.join("fabro.toml"),
+            r#"_version = 1
+
+[run.goal]
+file = "prompts/goal.md"
+"#,
+        )
+        .unwrap();
+        std::fs::write(project.join("prompts/goal.md"), "ship from project root").unwrap();
+
+        std::fs::write(
+            workflow_dir.join("workflow.toml"),
+            "_version = 1\n\n[workflow]\ngraph = \"workflow.fabro\"\n",
+        )
+        .unwrap();
+        std::fs::write(
+            workflow_dir.join("workflow.fabro"),
+            r"digraph Demo { start [shape=Mdiamond] exit [shape=Msquare] start -> exit }",
+        )
+        .unwrap();
+
+        let sandboxed_settings = temp.path().join("empty-settings.toml");
+        std::fs::write(&sandboxed_settings, "_version = 1\n").unwrap();
+        // SAFETY: single-threaded unit test body.
+        unsafe {
+            std::env::set_var("FABRO_CONFIG", &sandboxed_settings);
+        }
+
+        let built = build_run_manifest(ManifestBuildInput {
+            workflow: PathBuf::from("fabro/workflows/demo/workflow.toml"),
+            cwd: project.to_path_buf(),
+            args_layer: ConfigLayer::default(),
+            args: None,
+            run_id: None,
+        })
+        .unwrap();
+
+        // SAFETY: single-threaded unit test body.
+        unsafe {
+            std::env::remove_var("FABRO_CONFIG");
+        }
+
+        let goal = built.manifest.goal.expect("manifest goal should be set");
+        assert_eq!(goal.text, "ship from project root");
+        assert_eq!(goal.type_, types::ManifestGoalType::File);
+        let resolved = goal.path.expect("file goal must carry a path");
+        let expected = project.join("prompts").join("goal.md");
+        assert_eq!(PathBuf::from(resolved), expected);
+    }
+
+    /// A relative `[run.goal] file = "..."` declared in `workflow.toml`
+    /// must resolve against the directory of `workflow.toml`, not against
+    /// the invocation cwd or project root.
+    #[test]
+    #[allow(unsafe_code, clippy::allow_attributes)]
+    fn build_manifest_resolves_relative_goal_file_in_workflow_config() {
+        let temp = tempfile::tempdir().unwrap();
+        let project = temp.path();
+        let workflow_dir = project.join("fabro/workflows/demo");
+        std::fs::create_dir_all(workflow_dir.join("prompts")).unwrap();
+
+        std::fs::write(project.join("fabro.toml"), "_version = 1\n").unwrap();
+        std::fs::write(
+            workflow_dir.join("workflow.toml"),
+            r#"_version = 1
+
+[workflow]
+graph = "workflow.fabro"
+
+[run.goal]
+file = "prompts/goal.md"
+"#,
+        )
+        .unwrap();
+        std::fs::write(
+            workflow_dir.join("prompts/goal.md"),
+            "ship from workflow dir",
+        )
+        .unwrap();
+        std::fs::write(
+            workflow_dir.join("workflow.fabro"),
+            r"digraph Demo { start [shape=Mdiamond] exit [shape=Msquare] start -> exit }",
+        )
+        .unwrap();
+
+        let sandboxed_settings = temp.path().join("empty-settings.toml");
+        std::fs::write(&sandboxed_settings, "_version = 1\n").unwrap();
+        // SAFETY: single-threaded unit test body.
+        unsafe {
+            std::env::set_var("FABRO_CONFIG", &sandboxed_settings);
+        }
+
+        let built = build_run_manifest(ManifestBuildInput {
+            workflow: PathBuf::from("fabro/workflows/demo/workflow.toml"),
+            cwd: project.to_path_buf(),
+            args_layer: ConfigLayer::default(),
+            args: None,
+            run_id: None,
+        })
+        .unwrap();
+
+        // SAFETY: single-threaded unit test body.
+        unsafe {
+            std::env::remove_var("FABRO_CONFIG");
+        }
+
+        let goal = built.manifest.goal.expect("manifest goal should be set");
+        assert_eq!(goal.text, "ship from workflow dir");
+        assert_eq!(goal.type_, types::ManifestGoalType::File);
+        let resolved = goal.path.expect("file goal must carry a path");
+        let expected = workflow_dir.join("prompts").join("goal.md");
+        assert_eq!(PathBuf::from(resolved), expected);
+    }
 }
diff --git a/lib/crates/fabro-config/src/project.rs b/lib/crates/fabro-config/src/project.rs
index eb7e569a6..2c49cf426 100644
--- a/lib/crates/fabro-config/src/project.rs
+++ b/lib/crates/fabro-config/src/project.rs
@@ -33,10 +33,11 @@ pub fn parse_project_config(content: &str) -> anyhow::Result<ConfigLayer> {
 }
 
 /// Load a project config from a file path.
+///
+/// Goes through [`ConfigLayer::load`] so that relative `run.goal.file`
+/// paths are anchored at the directory of `path` at load time.
 pub fn load_project_config(path: &Path) -> anyhow::Result<ConfigLayer> {
-    let content = std::fs::read_to_string(path)
-        .with_context(|| format!("Failed to read {}", path.display()))?;
-    let config = parse_project_config(&content)?;
+    let config = ConfigLayer::load(path).context("Failed to parse project config")?;
     let root = config
         .as_v2()
         .project
@@ -477,4 +478,28 @@ retros = true
         assert_eq!(found_path, tmp.path().join("fabro.toml"));
         assert_eq!(config.as_v2().version, Some(1));
     }
+
+    #[test]
+    fn load_project_config_rewrites_relative_goal_file_path() {
+        use fabro_types::settings::run::RunGoalLayer;
+
+        let tmp = TempDir::new().unwrap();
+        let path = tmp.path().join("fabro.toml");
+        fs::write(
+            &path,
+            r#"_version = 1
+
+[run.goal]
+file = "prompts/goal.md"
+"#,
+        )
+        .unwrap();
+
+        let config = load_project_config(&path).unwrap();
+        let Some(RunGoalLayer::File { file }) = config.as_v2().run_goal_layer() else {
+            panic!("expected file variant");
+        };
+        let expected = tmp.path().join("prompts").join("goal.md");
+        assert_eq!(file.as_source(), expected.to_string_lossy());
+    }
 }
diff --git a/lib/crates/fabro-config/src/run.rs b/lib/crates/fabro-config/src/run.rs
index a5c015173..33fac41c4 100644
--- a/lib/crates/fabro-config/src/run.rs
+++ b/lib/crates/fabro-config/src/run.rs
@@ -18,11 +18,10 @@ pub fn parse_run_config(contents: &str) -> anyhow::Result<ConfigLayer> {
 
 /// Load and parse a run config from a TOML file.
 ///
-/// Returns the v2-backed `ConfigLayer`.
+/// Goes through [`ConfigLayer::load`] so that relative `run.goal.file`
+/// paths are anchored at the directory of `path` at load time.
 pub fn load_run_config(path: &Path) -> anyhow::Result<ConfigLayer> {
-    let content = std::fs::read_to_string(path)
-        .with_context(|| format!("Failed to read {}", path.display()))?;
-    ConfigLayer::parse(&content)
+    ConfigLayer::load(path)
         .with_context(|| format!("Failed to parse workflow config at {}", path.display()))
 }
 
@@ -34,3 +33,54 @@ pub fn resolve_graph_path(workflow_toml: &Path, graph_relative: &str) -> PathBuf
         .unwrap_or_else(|| Path::new("."))
         .join(graph_relative)
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use fabro_types::settings::run::RunGoalLayer;
+
+    #[test]
+    fn load_run_config_rewrites_relative_goal_file_path() {
+        let tmp = tempfile::tempdir().unwrap();
+        let workflow_dir = tmp.path().join("fabro").join("workflows").join("demo");
+        std::fs::create_dir_all(&workflow_dir).unwrap();
+        let workflow_toml = workflow_dir.join("workflow.toml");
+        std::fs::write(
+            &workflow_toml,
+            r#"_version = 1
+
+[run.goal]
+file = "prompts/goal.md"
+"#,
+        )
+        .unwrap();
+
+        let config = load_run_config(&workflow_toml).unwrap();
+        let Some(RunGoalLayer::File { file }) = config.as_v2().run_goal_layer() else {
+            panic!("expected file variant");
+        };
+        let expected = workflow_dir.join("prompts").join("goal.md");
+        assert_eq!(file.as_source(), expected.to_string_lossy());
+    }
+
+    #[test]
+    fn load_run_config_leaves_absolute_goal_file_untouched() {
+        let tmp = tempfile::tempdir().unwrap();
+        let workflow_toml = tmp.path().join("workflow.toml");
+        std::fs::write(
+            &workflow_toml,
+            r#"_version = 1
+
+[run.goal]
+file = "/etc/fabro/goal.md"
+"#,
+        )
+        .unwrap();
+
+        let config = load_run_config(&workflow_toml).unwrap();
+        let Some(RunGoalLayer::File { file }) = config.as_v2().run_goal_layer() else {
+            panic!("expected file variant");
+        };
+        assert_eq!(file.as_source(), "/etc/fabro/goal.md");
+    }
+}