diff --git a/easyunfold/cli.py b/easyunfold/cli.py
index b215f8d..75e3097 100644
--- a/easyunfold/cli.py
+++ b/easyunfold/cli.py
@@ -57,11 +57,16 @@ def easyunfold():
 @click.option('--out-file', '-o', default='easyunfold.json', help='Name of the output file')
 @click.option('--no-expand', help='Do not expand the kpoints by symmetry', default=False, is_flag=True)
 @click.option('--nk-per-split', help='Number of band structure kpoints per split.', type=int)
+@click.option('--separate-folders/--no-separate-folders',
+              help='Whether to use separate folders for each split.',
+              default=False,
+              show_default=True)
 @click.option('--scf-kpoints',
               help='File (IBZKPT) to provide SCF kpoints for self-consistent calculations. Needed for hybrid functional calculations.',
               type=click.Path(exists=True, dir_okay=False))
 @click.option('--yes', '-y', is_flag=True, default=False, help='Skip and confirmation.', hidden=True)  # hide help
-def generate(pc_file, code, sc_file, matrix, kpoints, time_reversal, out_file, no_expand, symprec, nk_per_split, scf_kpoints, yes):
+def generate(pc_file, code, sc_file, matrix, kpoints, time_reversal, out_file, no_expand, symprec, nk_per_split, scf_kpoints, yes,
+             separate_folders):
     """
     Generate the kpoints for performing supercell calculations.
 
@@ -155,6 +160,7 @@ def generate(pc_file, code, sc_file, matrix, kpoints, time_reversal, out_file, n
         out_kpt_name,
         nk_per_split=nk_per_split,
         scf_kpoints_and_weights=scf_kpoints_and_weights,
+        use_separate_folders=separate_folders,
         source=sc_file,
     )
 
diff --git a/easyunfold/unfold.py b/easyunfold/unfold.py
index 26d038c..42b036d 100644
--- a/easyunfold/unfold.py
+++ b/easyunfold/unfold.py
@@ -11,6 +11,7 @@
 import re
 import warnings
 from typing import Union, List, Tuple
+from pathlib import Path
 from packaging import version
 
 import numpy as np
@@ -332,6 +333,7 @@ def write_sc_kpoints(self,
                          file: str,
                          nk_per_split: Union[None, list] = None,
                          scf_kpoints_and_weights: Union[None, list] = None,
+                         use_separate_folders=False,
                          **kwargs):
         """
         Write the supercell kpoints to a file.
@@ -358,12 +360,13 @@ def write_sc_kpoints(self,
             for i_spilt, kpt in enumerate(splits):
                 if scf_kpoints_and_weights:
                     kpt, weights = concatenate_scf_kpoints(scf_kpoints_and_weights[0], scf_kpoints_and_weights[1], kpt)
-                write_kpoints(kpt,
-                              f'{file}_{i_spilt + 1:03d}',
-                              f'supercell kpoints split {i_spilt + 1}',
-                              code=self.dft_code,
-                              weights=weights,
-                              **kwargs)
+                if use_separate_folders:
+                    folder = f'split-{i_spilt+1:03d}'
+                    Path(folder).mkdir(exist_ok=True)
+                    fname = str(folder / file)
+                else:
+                    fname = f'{file}_{i_spilt + 1:03d}'
+                write_kpoints(kpt, fname, f'supercell kpoints split {i_spilt + 1}', code=self.dft_code, weights=weights, **kwargs)
 
     def write_pc_kpoints(self, file: str, expanded: bool = False, **kwargs):
         """Write the primitive cell kpoints"""