diff --git a/loki/batch/tests/test_transformation.py b/loki/batch/tests/test_transformation.py
index c41f1b843..c410441c1 100644
--- a/loki/batch/tests/test_transformation.py
+++ b/loki/batch/tests/test_transformation.py
@@ -414,22 +414,23 @@ def test_transformation_file_write(tmp_path):
 """
     source = Sourcefile.from_source(fcode)
     source.path = Path('rick.F90')
-    item = ProcedureItem(name='#rick', source=source)
+    item = ProcedureItem(name='#rick', source=source, config={'mode': 'roll'})
 
-    # Test default file writes
-    ricks_path = tmp_path/'rick.loki.F90'
+    # Test mode and suffix overrides
+    ricks_path = tmp_path/'rick.roll.java'
     if ricks_path.exists():
         ricks_path.unlink()
-    FileWriteTransformation().apply(source=source, item=item, build_args={'output_dir': tmp_path})
+    FileWriteTransformation(suffix='.java').apply(source=source, item=item,
+                                                  build_args={'output_dir': tmp_path})
     assert ricks_path.exists()
     ricks_path.unlink()
 
-    # Test mode and suffix overrides
-    ricks_path = tmp_path/'rick.roll.java'
+    item = ProcedureItem(name='#rick', source=source)
+    # Test default file writes
+    ricks_path = tmp_path/'rick.loki.F90'
     if ricks_path.exists():
         ricks_path.unlink()
-    FileWriteTransformation(mode='roll', suffix='.java').apply(source=source, item=item,
-                                                               build_args={'output_dir': tmp_path})
+    FileWriteTransformation().apply(source=source, item=item, build_args={'output_dir': tmp_path})
     assert ricks_path.exists()
     ricks_path.unlink()
 
diff --git a/loki/transformations/build_system/file_write.py b/loki/transformations/build_system/file_write.py
index 506e172d9..f9182d877 100644
--- a/loki/transformations/build_system/file_write.py
+++ b/loki/transformations/build_system/file_write.py
@@ -23,8 +23,6 @@ class FileWriteTransformation(Transformation):
 
     Parameters
     ----------
-    mode : str, optional
-        "Mode" identifier string to add in front of the file suffix
     suffix : str, optional
         File suffix to determine file type for all written file. If
         omitted, it will preserve the original file type.
@@ -39,10 +37,9 @@ class FileWriteTransformation(Transformation):
     traverse_file_graph = True
 
     def __init__(
-            self, mode='loki', suffix=None, cuf=False,
+            self, suffix=None, cuf=False,
             include_module_var_imports=False
     ):
-        self.mode = mode
         self.suffix = suffix
         self.cuf = cuf
         self.include_module_var_imports = include_module_var_imports
@@ -66,9 +63,12 @@ def transform_file(self, sourcefile, **kwargs):
         if not item:
             raise ValueError('No Item provided; required to determine file write path')
 
+        _mode = item.mode if item.mode else 'loki'
+        _mode = _mode.replace('-', '_')  # Sanitize mode string
+
         path = Path(item.path)
         suffix = self.suffix if self.suffix else path.suffix
-        sourcepath = Path(item.path).with_suffix(f'.{self.mode}{suffix}')
+        sourcepath = Path(item.path).with_suffix(f'.{_mode}{suffix}')
         build_args = kwargs.get('build_args', {})
         if build_args and (output_dir := build_args.get('output_dir', None)) is not None:
             sourcepath = Path(output_dir)/sourcepath.name
diff --git a/scripts/loki_transform.py b/scripts/loki_transform.py
index f39005bc2..2309d903e 100644
--- a/scripts/loki_transform.py
+++ b/scripts/loki_transform.py
@@ -140,6 +140,9 @@ def convert(
 
     config = SchedulerConfig.from_file(config)
 
+    # set default transformation mode in Scheduler config
+    config.default['mode'] = mode
+
     directive = None if directive.lower() == 'none' else directive.lower()
 
     build_args = {
@@ -186,7 +189,7 @@ def convert(
         # Write out all modified source files into the build directory
         file_write_trafo = scheduler.config.transformations.get('FileWriteTransformation', None)
         if not file_write_trafo:
-            file_write_trafo = FileWriteTransformation(mode=mode, cuf='cuf' in mode)
+            file_write_trafo = FileWriteTransformation(cuf='cuf' in mode)
         scheduler.process(transformation=file_write_trafo)
 
         return
@@ -406,8 +409,7 @@ def convert(
 
     # Write out all modified source files into the build directory
     scheduler.process(transformation=FileWriteTransformation(
-        mode=mode, cuf='cuf' in mode,
-        include_module_var_imports=global_var_offload
+        cuf='cuf' in mode, include_module_var_imports=global_var_offload
     ))