diff --git a/src/metadata.rs b/src/metadata.rs
index 66342b73e..c256f1ce2 100644
--- a/src/metadata.rs
+++ b/src/metadata.rs
@@ -356,7 +356,13 @@ impl Metadata21 {
             gui_scripts: HashMap::new(),
             entry_points: HashMap::new(),
         };
-        metadata.merge_pyproject_toml(manifest_path)?;
+
+        let manifest_path = manifest_path.as_ref();
+        let py_src = extra_metadata
+            .python_source
+            .map(|src| manifest_path.join(src))
+            .unwrap_or_else(|| manifest_path.to_path_buf());
+        metadata.merge_pyproject_toml(py_src)?;
         Ok(metadata)
     }
 
@@ -776,4 +782,20 @@ mod test {
         let pkginfo: Result<python_pkginfo::Metadata, _> = content.parse();
         assert!(pkginfo.is_ok());
     }
+
+    #[test]
+    fn test_merge_metadata_from_pyproject_toml_with_customized_python_source_dir() {
+        let cargo_toml_str =
+            fs_err::read_to_string("test-crates/pyo3-mixed-py-subdir/Cargo.toml").unwrap();
+        let cargo_toml: CargoToml = toml::from_str(&cargo_toml_str).unwrap();
+        let metadata =
+            Metadata21::from_cargo_toml(&cargo_toml, "test-crates/pyo3-mixed-py-subdir").unwrap();
+        // defined in Cargo.toml
+        assert_eq!(
+            metadata.summary,
+            Some("Implements a dummy function combining rust and python".to_string())
+        );
+        // defined in pyproject.toml
+        assert_eq!(metadata.scripts["get_42"], "pyo3_mixed_py_subdir:get_42");
+    }
 }
diff --git a/test-crates/pyo3-mixed-py-subdir/pyproject.toml b/test-crates/pyo3-mixed-py-subdir/python/pyproject.toml
similarity index 100%
rename from test-crates/pyo3-mixed-py-subdir/pyproject.toml
rename to test-crates/pyo3-mixed-py-subdir/python/pyproject.toml