diff --git a/flow360/component/simulation/framework/updater.py b/flow360/component/simulation/framework/updater.py
index 7f206e7b2..574dcc9c1 100644
--- a/flow360/component/simulation/framework/updater.py
+++ b/flow360/component/simulation/framework/updater.py
@@ -636,6 +636,23 @@ def fix_write_single_file_for_paraview_format(params_as_dict):
     return params_as_dict
 
 
+def _to_25_9_0(params_as_dict):
+    """
+    Remove deprecated meshing defaults key `remove_non_manifold_faces`.
+
+    Note: this function is intentionally not registered in VERSION_MILESTONES until
+    the Python client version reaches 25.9.0.
+    """
+    meshing = params_as_dict.get("meshing")
+    if not isinstance(meshing, dict):
+        return params_as_dict
+    meshing_defaults = meshing.get("defaults")
+    if not isinstance(meshing_defaults, dict):
+        return params_as_dict
+    meshing_defaults.pop("remove_non_manifold_faces", None)
+    return params_as_dict
+
+
 VERSION_MILESTONES = [
     (Flow360Version("24.11.1"), _to_24_11_1),
     (Flow360Version("24.11.7"), _to_24_11_7),
diff --git a/flow360/component/simulation/meshing_param/meshing_specs.py b/flow360/component/simulation/meshing_param/meshing_specs.py
index cd4ab0344..89560a6f5 100644
--- a/flow360/component/simulation/meshing_param/meshing_specs.py
+++ b/flow360/component/simulation/meshing_param/meshing_specs.py
@@ -19,6 +19,7 @@
     ConditionalField,
     ContextField,
     ParamsValidationInfo,
+    add_validation_warning,
     contextual_field_validator,
 )
 from flow360.component.simulation.validation.validation_utils import (
@@ -159,12 +160,6 @@ class MeshingDefaults(Flow360BaseModel):
         + "per face with :class:`~flow360.GeometryRefinement`.",
     )
 
-    remove_non_manifold_faces: bool = pd.Field(
-        False,
-        description="Flag to remove non-manifold and interior faces. "
-        + "This option is only supported when using geometry AI.",
-    )
-
     remove_hidden_geometry: bool = pd.Field(
         False,
         description="Flag to remove hidden geometry that is not visible to flow. "
@@ -178,6 +173,28 @@ class MeshingDefaults(Flow360BaseModel):
         + "This option is only supported when using geometry AI.",
     )
 
+    @pd.model_validator(mode="before")
+    @classmethod
+    def remove_deprecated_arguments(cls, value):
+        """
+        Detect when invoking the constructor of the MeshingDefaults()
+        (Warning: contrary to deserializing data, which is supposed to be handled by the updater.py)
+        If the user added the remove_non_manifold_faces in the argument, pop the argument and give warning
+        that this is no longer supported.
+        """
+        if not isinstance(value, dict):
+            return value
+
+        if "remove_non_manifold_faces" in value:
+            value.pop("remove_non_manifold_faces", None)
+            message = (
+                "`meshing.defaults.remove_non_manifold_faces` is no longer supported and has been "
+                + "ignored. Set `meshing.defaults.remove_hidden_geometry` instead."
+            )
+            add_validation_warning(message)
+
+        return value
+
     @contextual_field_validator("number_of_boundary_layers", mode="after")
     @classmethod
     def invalid_number_of_boundary_layers(cls, value, param_info: ParamsValidationInfo):
@@ -203,7 +220,6 @@ def invalid_geometry_accuracy(cls, value, param_info: ParamsValidationInfo):
         "resolve_face_boundaries",
         "preserve_thin_geometry",
         "sealing_size",
-        "remove_non_manifold_faces",
         "remove_hidden_geometry",
         "flooding_cell_size",
         mode="after",
@@ -213,16 +229,6 @@ def ensure_geometry_ai_features(cls, value, info, param_info: ParamsValidationIn
         """Validate that the feature is only used when Geometry AI is enabled."""
         return check_geometry_ai_features(cls, value, info, param_info)
 
-    @pd.model_validator(mode="after")
-    def validate_mutual_exclusion(self):
-        """Ensure remove_non_manifold_faces and remove_hidden_geometry are not both True."""
-        if self.remove_non_manifold_faces and self.remove_hidden_geometry:
-            raise ValueError(
-                "'remove_non_manifold_faces' and 'remove_hidden_geometry' cannot both be True. "
-                "Please enable only one of these options."
-            )
-        return self
-
     @pd.model_validator(mode="after")
     def validate_flooding_cell_size_requires_remove_hidden_geometry(self):
         """Ensure flooding_cell_size is only specified when remove_hidden_geometry is True."""
diff --git a/flow360/component/simulation/translator/surface_meshing_translator.py b/flow360/component/simulation/translator/surface_meshing_translator.py
index 6ea7fd9bb..1640fd586 100644
--- a/flow360/component/simulation/translator/surface_meshing_translator.py
+++ b/flow360/component/simulation/translator/surface_meshing_translator.py
@@ -726,7 +726,6 @@ def _get_gai_setting_whitelist(input_params: SimulationParams) -> dict:
         "surface_max_aspect_ratio": None,
         "surface_max_adaptation_iterations": None,
         "sealing_size": None,
-        "remove_non_manifold_faces": None,
         "remove_hidden_geometry": None,
         "flooding_cell_size": None,
         "planar_face_tolerance": None,
diff --git a/tests/ref/simulation/service_init_geometry.json b/tests/ref/simulation/service_init_geometry.json
index a72e06dde..4435b646c 100644
--- a/tests/ref/simulation/service_init_geometry.json
+++ b/tests/ref/simulation/service_init_geometry.json
@@ -23,7 +23,6 @@
                 "units": "m"
             },
             "sliding_interface_tolerance": 0.01,
-            "remove_non_manifold_faces": false,
             "remove_hidden_geometry": false
         },
         "outputs": [],
diff --git a/tests/ref/simulation/service_init_surface_mesh.json b/tests/ref/simulation/service_init_surface_mesh.json
index 3fec243f8..b066d9c7e 100644
--- a/tests/ref/simulation/service_init_surface_mesh.json
+++ b/tests/ref/simulation/service_init_surface_mesh.json
@@ -23,7 +23,6 @@
                 "units": "m"
             },
             "sliding_interface_tolerance": 0.01,
-            "remove_non_manifold_faces": false,
             "remove_hidden_geometry": false
         },
         "outputs": [],
diff --git a/tests/simulation/data/geometry_airplane/simulation.json b/tests/simulation/data/geometry_airplane/simulation.json
index 52725caef..fadf4b412 100644
--- a/tests/simulation/data/geometry_airplane/simulation.json
+++ b/tests/simulation/data/geometry_airplane/simulation.json
@@ -30,8 +30,7 @@
             "sealing_size": {
                 "value": 0.0,
                 "units": "m"
-            },
-            "remove_non_manifold_faces": false
+            }
         },
         "refinements": [
             {
@@ -2539,4 +2538,4 @@
         "use_inhouse_mesher": false,
         "use_geometry_AI": false
     }
-}
\ No newline at end of file
+}
diff --git a/tests/simulation/params/meshing_validation/test_meshing_param_validation.py b/tests/simulation/params/meshing_validation/test_meshing_param_validation.py
index a14fbd572..c20932373 100644
--- a/tests/simulation/params/meshing_validation/test_meshing_param_validation.py
+++ b/tests/simulation/params/meshing_validation/test_meshing_param_validation.py
@@ -1537,62 +1537,6 @@ def test_wind_tunnel_farfield_requires_geometry_ai():
             assert farfield.type == "WindTunnelFarfield"
 
 
-def test_remove_non_manifold_faces_and_remove_hidden_geometry_mutual_exclusion():
-    """Test that remove_non_manifold_faces and remove_hidden_geometry cannot both be True."""
-    gai_context = ParamsValidationInfo({}, [])
-    gai_context.use_geometry_AI = True
-
-    # Test 1: Both True should raise ValueError
-    with pytest.raises(
-        pd.ValidationError,
-        match=r"'remove_non_manifold_faces' and 'remove_hidden_geometry' cannot both be True",
-    ):
-        with ValidationContext(SURFACE_MESH, gai_context):
-            with SI_unit_system:
-                MeshingDefaults(
-                    geometry_accuracy=0.01 * u.m,
-                    surface_max_edge_length=0.1 * u.m,
-                    remove_non_manifold_faces=True,
-                    remove_hidden_geometry=True,
-                )
-
-    # Test 2: Only remove_non_manifold_faces=True should work
-    with ValidationContext(SURFACE_MESH, gai_context):
-        with SI_unit_system:
-            defaults = MeshingDefaults(
-                geometry_accuracy=0.01 * u.m,
-                surface_max_edge_length=0.1 * u.m,
-                remove_non_manifold_faces=True,
-                remove_hidden_geometry=False,
-            )
-            assert defaults.remove_non_manifold_faces is True
-            assert defaults.remove_hidden_geometry is False
-
-    # Test 3: Only remove_hidden_geometry=True should work
-    with ValidationContext(SURFACE_MESH, gai_context):
-        with SI_unit_system:
-            defaults = MeshingDefaults(
-                geometry_accuracy=0.01 * u.m,
-                surface_max_edge_length=0.1 * u.m,
-                remove_non_manifold_faces=False,
-                remove_hidden_geometry=True,
-            )
-            assert defaults.remove_non_manifold_faces is False
-            assert defaults.remove_hidden_geometry is True
-
-    # Test 4: Both False should work (default case)
-    with ValidationContext(SURFACE_MESH, gai_context):
-        with SI_unit_system:
-            defaults = MeshingDefaults(
-                geometry_accuracy=0.01 * u.m,
-                surface_max_edge_length=0.1 * u.m,
-                remove_non_manifold_faces=False,
-                remove_hidden_geometry=False,
-            )
-            assert defaults.remove_non_manifold_faces is False
-            assert defaults.remove_hidden_geometry is False
-
-
 def test_flooding_cell_size_requires_remove_hidden_geometry():
     """Test that flooding_cell_size can only be specified when remove_hidden_geometry is True."""
     gai_context = ParamsValidationInfo({}, [])
diff --git a/tests/simulation/params/test_meshing_defaults_deprecation.py b/tests/simulation/params/test_meshing_defaults_deprecation.py
new file mode 100644
index 000000000..7b40eb583
--- /dev/null
+++ b/tests/simulation/params/test_meshing_defaults_deprecation.py
@@ -0,0 +1,19 @@
+from flow360.component.simulation.meshing_param.meshing_specs import MeshingDefaults
+from flow360.component.simulation.validation.validation_context import (
+    CASE,
+    ValidationContext,
+)
+
+
+def test_meshing_defaults_removes_deprecated_remove_non_manifold_faces():
+    payload = {"remove_non_manifold_faces": False}
+
+    with ValidationContext(levels=CASE) as validation_context:
+        defaults = MeshingDefaults.model_validate(payload)
+
+    dumped = defaults.model_dump(mode="json", by_alias=True)
+    assert "remove_non_manifold_faces" not in dumped
+
+    warning_messages = [warning["msg"] for warning in validation_context.validation_warnings]
+    assert len(warning_messages) == 1
+    assert "remove_non_manifold_faces" in warning_messages[0]
diff --git a/tests/simulation/service/data/dependency_geometry_sphere1_simulation.json b/tests/simulation/service/data/dependency_geometry_sphere1_simulation.json
index 18b32130f..6a6296b76 100644
--- a/tests/simulation/service/data/dependency_geometry_sphere1_simulation.json
+++ b/tests/simulation/service/data/dependency_geometry_sphere1_simulation.json
@@ -9,7 +9,6 @@
             },
             "planar_face_tolerance": 1e-06,
             "preserve_thin_geometry": false,
-            "remove_non_manifold_faces": false,
             "resolve_face_boundaries": false,
             "sealing_size": {
                 "units": "m",
diff --git a/tests/simulation/service/data/dependency_geometry_sphere2_simulation.json b/tests/simulation/service/data/dependency_geometry_sphere2_simulation.json
index 2a76b7dd8..528e723ee 100644
--- a/tests/simulation/service/data/dependency_geometry_sphere2_simulation.json
+++ b/tests/simulation/service/data/dependency_geometry_sphere2_simulation.json
@@ -9,7 +9,6 @@
             },
             "planar_face_tolerance": 1e-06,
             "preserve_thin_geometry": false,
-            "remove_non_manifold_faces": false,
             "resolve_face_boundaries": false,
             "sealing_size": {
                 "units": "m",
diff --git a/tests/simulation/service/data/root_geometry_cube_simulation.json b/tests/simulation/service/data/root_geometry_cube_simulation.json
index 880212b27..faab23101 100644
--- a/tests/simulation/service/data/root_geometry_cube_simulation.json
+++ b/tests/simulation/service/data/root_geometry_cube_simulation.json
@@ -9,7 +9,6 @@
             },
             "planar_face_tolerance": 1e-06,
             "preserve_thin_geometry": false,
-            "remove_non_manifold_faces": false,
             "resolve_face_boundaries": false,
             "sealing_size": {
                 "units": "m",
diff --git a/tests/simulation/test_updater.py b/tests/simulation/test_updater.py
index 3214905ca..58a2ee301 100644
--- a/tests/simulation/test_updater.py
+++ b/tests/simulation/test_updater.py
@@ -10,6 +10,7 @@
 from flow360.component.simulation.framework.updater import (
     VERSION_MILESTONES,
     _find_update_path,
+    _to_25_9_0,
     updater,
 )
 from flow360.component.simulation.framework.updater_utils import Flow360Version
@@ -1582,3 +1583,22 @@ def test_updater_to_25_8_4_write_single_file_false():
     assert (
         params_new["outputs"][0]["write_single_file"] is False
     ), "write_single_file should remain False"
+
+
+def test_updater_to_25_9_0_remove_deprecated_remove_non_manifold_faces():
+    """Test 25.9.0 updater step removes deprecated meshing.defaults.remove_non_manifold_faces key."""
+
+    params_as_dict = {
+        "version": "25.8.3",
+        "unit_system": {"name": "SI"},
+        "meshing": {
+            "defaults": {
+                "surface_max_edge_length": {"value": 0.2, "units": "m"},
+                "remove_non_manifold_faces": False,
+            }
+        },
+    }
+
+    params_new = _to_25_9_0(params_as_dict)
+    defaults = params_new["meshing"]["defaults"]
+    assert "remove_non_manifold_faces" not in defaults
diff --git a/tests/simulation/translator/data/gai_windtunnel_farfield_info/simulation.json b/tests/simulation/translator/data/gai_windtunnel_farfield_info/simulation.json
index f63c753af..6fc2ea9af 100644
--- a/tests/simulation/translator/data/gai_windtunnel_farfield_info/simulation.json
+++ b/tests/simulation/translator/data/gai_windtunnel_farfield_info/simulation.json
@@ -30,8 +30,7 @@
             "sealing_size": {
                 "value": 0.0,
                 "units": "m"
-            },
-            "remove_non_manifold_faces": false
+            }
         },
         "refinements": [],
         "volume_zones": [
@@ -969,4 +968,4 @@
         "use_inhouse_mesher": true,
         "use_geometry_AI": true
     }
-}
\ No newline at end of file
+}
diff --git a/tests/simulation/translator/ref/Flow360_mirrored_surface_meshing.json b/tests/simulation/translator/ref/Flow360_mirrored_surface_meshing.json
index 7fe9c5f14..58ab0ecad 100644
--- a/tests/simulation/translator/ref/Flow360_mirrored_surface_meshing.json
+++ b/tests/simulation/translator/ref/Flow360_mirrored_surface_meshing.json
@@ -11,7 +11,6 @@
             },
             "planar_face_tolerance": 1e-06,
             "preserve_thin_geometry": false,
-            "remove_non_manifold_faces": false,
             "remove_hidden_geometry": false,
             "resolve_face_boundaries": false,
             "sealing_size": {
diff --git a/tests/simulation/translator/ref/surface_meshing/gai_surface_mesher.json b/tests/simulation/translator/ref/surface_meshing/gai_surface_mesher.json
index a1b9fbdf6..653d6bd31 100644
--- a/tests/simulation/translator/ref/surface_meshing/gai_surface_mesher.json
+++ b/tests/simulation/translator/ref/surface_meshing/gai_surface_mesher.json
@@ -22,7 +22,6 @@
                 "value": 0.0,
                 "units": "1.0*m"
             },
-            "remove_non_manifold_faces": false,
             "remove_hidden_geometry": false,
             "planar_face_tolerance": 1e-06
         },
diff --git a/tests/simulation/translator/ref/surface_meshing/gai_windtunnel.json b/tests/simulation/translator/ref/surface_meshing/gai_windtunnel.json
index e15c2b681..662590b76 100644
--- a/tests/simulation/translator/ref/surface_meshing/gai_windtunnel.json
+++ b/tests/simulation/translator/ref/surface_meshing/gai_windtunnel.json
@@ -22,7 +22,6 @@
                 "value": 0.0,
                 "units": "1.0*m"
             },
-            "remove_non_manifold_faces": false,
             "remove_hidden_geometry": false,
             "planar_face_tolerance": 0.001
         },