diff --git a/src/uu/cp/src/cp.rs b/src/uu/cp/src/cp.rs
index c6c8789e2..9ef767d05 100644
--- a/src/uu/cp/src/cp.rs
+++ b/src/uu/cp/src/cp.rs
@@ -1375,10 +1375,19 @@ pub fn copy(sources: &[PathBuf], target: &Path, options: &Options) -> CopyResult
             {
                 // There is already a file and it isn't a symlink (managed in a different place)
                 if copied_destinations.contains(&dest) && options.backup != BackupMode::Numbered {
-                    // If the target file was already created in this cp call, do not overwrite
-                    return Err(CpError::Error(
-                        translate!("cp-error-will-not-overwrite-just-created", "dest" => dest.quote(), "source" => source.quote()),
-                    ));
+                    // If the target was already created in this cp call, check if it's a directory.
+                    // Directories should be merged (GNU cp behavior), but files should not be overwritten.
+                    let dest_is_dir = fs::metadata(&dest).is_ok_and(|m| m.is_dir());
+                    let source_is_dir = fs::metadata(source).is_ok_and(|m| m.is_dir());
+
+                    // Only prevent overwriting if both source and dest are files (not directories)
+                    // Directories should be merged, which is handled by copy_directory
+                    if !dest_is_dir || !source_is_dir {
+                        // If the target file was already created in this cp call, do not overwrite
+                        return Err(CpError::Error(
+                            translate!("cp-error-will-not-overwrite-just-created", "dest" => dest.quote(), "source" => source.quote()),
+                        ));
+                    }
                 }
             }
 
diff --git a/tests/by-util/test_cp.rs b/tests/by-util/test_cp.rs
index 3c5b3242e..c6f0d1c77 100644
--- a/tests/by-util/test_cp.rs
+++ b/tests/by-util/test_cp.rs
@@ -142,6 +142,41 @@ fn test_cp_duplicate_folder() {
     assert!(at.dir_exists(format!("{TEST_COPY_TO_FOLDER}/{TEST_COPY_FROM_FOLDER}").as_str()));
 }
 
+#[test]
+fn test_cp_duplicate_directories_merge() {
+    let (at, mut ucmd) = at_and_ucmd!();
+
+    // Source directory 1
+    at.mkdir_all("src_dir/subdir");
+    at.write("src_dir/subdir/file1.txt", "content1");
+    at.write("src_dir/subdir/file2.txt", "content2");
+
+    // Source directory 2
+    at.mkdir_all("src_dir2/subdir");
+    at.write("src_dir2/subdir/file1.txt", "content3");
+
+    // Destination
+    at.mkdir("dest");
+
+    // Perform merge copy
+    ucmd.arg("-r")
+        .arg("src_dir/subdir")
+        .arg("src_dir2/subdir")
+        .arg("dest")
+        .succeeds();
+
+    // Verify directory exists
+    assert!(at.dir_exists("dest/subdir"));
+
+    // file1.txt should be overwritten by src_dir2/subdir/file1.txt
+    assert!(at.file_exists("dest/subdir/file1.txt"));
+    assert_eq!(at.read("dest/subdir/file1.txt"), "content3");
+
+    // file2.txt should remain from first copy
+    assert!(at.file_exists("dest/subdir/file2.txt"));
+    assert_eq!(at.read("dest/subdir/file2.txt"), "content2");
+}
+
 #[test]
 fn test_cp_duplicate_files_normalized_path() {
     let (at, mut ucmd) = at_and_ucmd!();