diff --git a/src/aiidalab_qe/app/configuration/advanced.py b/src/aiidalab_qe/app/configuration/advanced.py
index a311eda7..50c07995 100644
--- a/src/aiidalab_qe/app/configuration/advanced.py
+++ b/src/aiidalab_qe/app/configuration/advanced.py
@@ -27,7 +27,9 @@ class AdvancedSettings(Panel):
         """<div style="padding-top: 0px; padding-bottom: 10px">
         <h4>Advanced Settings</h4></div>"""
     )
-    description = ipw.HTML("""Select the advanced settings for the <b>pw.x</b> code.""")
+    pw_adv_description = ipw.HTML(
+        """Select the advanced settings for the <b>pw.x</b> code."""
+    )
     kpoints_description = ipw.HTML(
         """<div>
         The k-points mesh density of the SCF calculation is set by the <b>protocol</b>.
@@ -47,6 +49,18 @@ class AdvancedSettings(Panel):
     def __init__(self, default_protocol=None, **kwargs):
         self._default_protocol = default_protocol or DEFAULT_PARAMETERS["protocol"]
 
+        # clean-up workchain settings
+        self.clean_workdir = ipw.Checkbox(
+            description="",
+            indent=False,
+            value=True,
+            layout=ipw.Layout(max_width="20px"),
+        )
+        self.clean_workdir_description = ipw.HTML(
+            """<div style="line-height: 140%; padding-top: 0px; padding-bottom: 5px">
+            Tick to clean-up the work directory after the calculation is finished.</div>"""
+        )
+
         # Override setting widget
         self.override_prompt = ipw.HTML("<b>&nbsp;&nbsp;Override&nbsp;</b>")
         self.override = ipw.Checkbox(
@@ -120,7 +134,11 @@ def __init__(self, default_protocol=None, **kwargs):
         self.children = [
             self.title,
             ipw.HBox(
-                [self.description, self.override_widget],
+                [self.clean_workdir, self.clean_workdir_description],
+                layout=ipw.Layout(height="50px", justify_content="flex-start"),
+            ),
+            ipw.HBox(
+                [self.pw_adv_description, self.override_widget],
                 layout=ipw.Layout(height="50px", justify_content="space-between"),
             ),
             # total charge setting widget
@@ -193,6 +211,7 @@ def update_settings(self, **kwargs):
 
     def get_panel_value(self):
         # create the the initial_magnetic_moments as None (Default)
+        # XXX: start from parameters = {} and then bundle the settings by purposes (e.g. pw, bands, etc.)
         parameters = {
             "initial_magnetic_moments": None,
             "pw": {
@@ -201,6 +220,10 @@ def get_panel_value(self):
                 },
             },
         }
+        # add clean_workdir to the parameters
+        parameters["clean_workdir"] = self.clean_workdir.value
+
+        # add the pseudo_family to the parameters
         parameters["pseudo_family"] = self.pseudo_family_selector.value
         if self.pseudo_setter.pseudos:
             parameters["pw"]["pseudos"] = self.pseudo_setter.pseudos
diff --git a/src/aiidalab_qe/workflows/__init__.py b/src/aiidalab_qe/workflows/__init__.py
index 4f9236ad..0d1eb99f 100644
--- a/src/aiidalab_qe/workflows/__init__.py
+++ b/src/aiidalab_qe/workflows/__init__.py
@@ -52,7 +52,7 @@ def define(cls, spec):
         super().define(spec)
         spec.input('structure', valid_type=StructureData,
                    help='The inputs structure.')
-        spec.input('clean_workdir', valid_type=orm.Bool, default=lambda: orm.Bool(False),
+        spec.input('clean_workdir', valid_type=orm.Bool, default=lambda: orm.Bool(True),
                    help='If `True`, work directories of all called calculation will be cleaned at the end of execution.')
         spec.input('properties', valid_type=orm.List, default=lambda: orm.List(),
                    help='The properties to calculate, used to control the logic of QeAppWorkChain.')
@@ -111,7 +111,6 @@ def get_builder_from_protocol(
         cls,
         structure,
         parameters=None,
-        clean_workdir=False,
         **kwargs,
     ):
         """Return a builder prepopulated with inputs selected according to the chosen protocol."""
@@ -161,6 +160,9 @@ def get_builder_from_protocol(
             else:
                 builder.pop(name, None)
 
+        # XXX (unkcpz) I smell not proper design here since I have to look at
+        # configuration step to know what show be set here.
+        clean_workdir = parameters["advanced"]["clean_workdir"]
         builder.clean_workdir = orm.Bool(clean_workdir)
 
         return builder
diff --git a/tests/conftest.py b/tests/conftest.py
index 796d29af..1c03dd7e 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -293,7 +293,7 @@ def _smearing_settings_generator(**kwargs):
 
 
 @pytest.fixture
-def app(pw_code, dos_code, projwfc_code, sssp):
+def app(pw_code, dos_code, projwfc_code):
     from aiidalab_qe.app.main import App
 
     app = App(qe_auto_setup=False)
@@ -321,8 +321,6 @@ def app(pw_code, dos_code, projwfc_code, sssp):
 def submit_app_generator(
     app,
     generate_structure_data,
-    workchain_settings_generator,
-    smearing_settings_generator,
 ):
     """Return a function that generates a submit step widget."""
 
diff --git a/tests/test_configure.py b/tests/test_configure.py
index abe5547e..4e677afa 100644
--- a/tests/test_configure.py
+++ b/tests/test_configure.py
@@ -16,7 +16,6 @@ def test_get_configuration_parameters():
 
     wg = ConfigureQeAppWorkChainStep()
     parameters = wg.get_configuration_parameters()
-    print("parameters:", parameters)
     parameters_ref = {
         "workchain": wg.workchain_settings.get_panel_value(),
         "advanced": wg.advanced_settings.get_panel_value(),
diff --git a/tests/test_submit_qe_workchain/test_create_builder_default.yml b/tests/test_submit_qe_workchain/test_create_builder_default.yml
index b2af426f..49de55d6 100644
--- a/tests/test_submit_qe_workchain/test_create_builder_default.yml
+++ b/tests/test_submit_qe_workchain/test_create_builder_default.yml
@@ -57,7 +57,7 @@ bands:
           tot_charge: 0.0
       pseudos:
         Si: Si.upf
-clean_workdir: false
+clean_workdir: true
 pdos:
   dos:
     parameters: