diff --git a/src/aiida_shell/calculations/shell.py b/src/aiida_shell/calculations/shell.py
index 078d200..da62e7d 100644
--- a/src/aiida_shell/calculations/shell.py
+++ b/src/aiida_shell/calculations/shell.py
@@ -10,7 +10,7 @@
 from aiida.common.datastructures import CalcInfo, CodeInfo, FileCopyOperation
 from aiida.common.folders import Folder
 from aiida.engine import CalcJob, CalcJobProcessSpec
-from aiida.orm import Data, Dict, FolderData, List, RemoteData, SinglefileData, to_aiida_type
+from aiida.orm import Computer, Data, Dict, FolderData, List, RemoteData, SinglefileData, to_aiida_type
 from aiida.parsers import Parser
 
 from aiida_shell.data import EntryPointData, PickledData
@@ -281,9 +281,11 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
             inputs = {}
 
         nodes = inputs.get('nodes', {})
+        computer = inputs['code'].computer
         filenames = (inputs.get('filenames', None) or Dict()).get_dict()
         arguments = (inputs.get('arguments', None) or List()).get_list()
         outputs = (inputs.get('outputs', None) or List()).get_list()
+        use_symlinks = inputs['metadata']['options']['use_symlinks']
         filename_stdin = inputs['metadata']['options'].get('filename_stdin', None)
         filename_stdout = inputs['metadata']['options'].get('output_filename', None)
         default_retrieved_temporary = list(self.DEFAULT_RETRIEVED_TEMPORARY)
@@ -300,7 +302,10 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         if filename_stdin and filename_stdin in processed_arguments:
             processed_arguments.remove(filename_stdin)
 
-        remote_copy_list, remote_symlink_list = self.handle_remote_data_nodes(inputs)
+        remote_data_nodes = {key: node for key, node in nodes.items() if isinstance(node, RemoteData)}
+        remote_copy_list, remote_symlink_list = self.handle_remote_data_nodes(
+            remote_data_nodes, filenames, computer, use_symlinks
+        )
 
         code_info = CodeInfo()
         code_info.code_uuid = inputs['code'].uuid
@@ -329,16 +334,22 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         return calc_info
 
     @staticmethod
-    def handle_remote_data_nodes(inputs: dict[str, Data]) -> tuple[list[t.Any], list[t.Any]]:
-        """Handle a ``RemoteData`` that was passed in the ``nodes`` input.
+    def handle_remote_data_nodes(
+        remote_data_nodes: dict[str, RemoteData], filenames: dict[str, str], computer: Computer, use_symlinks: bool
+    ) -> tuple[list[t.Any], list[t.Any]]:
+        """Handle all ``RemoteData`` nodes that were passed in the ``nodes`` input.
 
-        :param inputs: The inputs dictionary.
+        :param remote_data_nodes: The ``RemoteData`` input nodes.
+        :param filenames: A dictionary of explicit filenames to use for the ``nodes`` to be written to ``dirpath``.
         :returns: A tuple of two lists, the ``remote_copy_list`` and the ``remote_symlink_list``.
         """
-        use_symlinks: bool = inputs['metadata']['options']['use_symlinks']  # type: ignore[index]
-        computer_uuid = inputs['code'].computer.uuid  # type: ignore[union-attr]
-        remote_nodes = [node for node in inputs.get('nodes', {}).values() if isinstance(node, RemoteData)]
-        instructions = [(computer_uuid, f'{node.get_remote_path()}/*', '.') for node in remote_nodes]
+        instructions = []
+
+        for key, node in remote_data_nodes.items():
+            if key in filenames:
+                instructions.append((computer.uuid, node.get_remote_path(), filenames[key]))
+            else:
+                instructions.append((computer.uuid, f'{node.get_remote_path()}/*', '.'))
 
         if use_symlinks:
             return [], instructions
@@ -407,7 +418,10 @@ def process_arguments_and_nodes(
                 self.write_folder_data(node, dirpath, filename)
                 argument_interpolated = argument.format(**{placeholder: filename or placeholder})
             elif isinstance(node, RemoteData):
-                self.handle_remote_data(node)
+                # Only the placeholder needs to be formatted. The content of the remote data itself is handled by the
+                # engine through the instructions created in ``handle_remote_data_nodes``.
+                filename = prepared_filenames[placeholder]
+                argument_interpolated = argument.format(**{placeholder: filename or placeholder})
             else:
                 argument_interpolated = argument.format(**{placeholder: str(node.value)})
 
@@ -465,6 +479,8 @@ def prepare_filenames(self, nodes: dict[str, SinglefileData], filenames: dict[st
                         raise RuntimeError(
                             f'node `{key}` contains the file `{f}` which overlaps with a reserved output filename.'
                         )
+            elif isinstance(node, RemoteData):
+                filename = filenames.get(key, None)
             else:
                 continue
 
diff --git a/tests/calculations/test_shell.py b/tests/calculations/test_shell.py
index c5c88f1..c1b6531 100644
--- a/tests/calculations/test_shell.py
+++ b/tests/calculations/test_shell.py
@@ -88,7 +88,7 @@ def test_nodes_folder_data(generate_calc_job, generate_code, tmp_path):
 
 @pytest.mark.parametrize('use_symlinks', (True, False))
 def test_nodes_remote_data(generate_calc_job, generate_code, tmp_path, aiida_localhost, use_symlinks):
-    """Test the ``nodes`` input with ``RemoteData`` nodes ."""
+    """Test the ``nodes`` input with ``RemoteData`` nodes."""
     inputs = {
         'code': generate_code(),
         'arguments': [],
@@ -107,6 +107,39 @@ def test_nodes_remote_data(generate_calc_job, generate_code, tmp_path, aiida_loc
         assert sorted(calc_info.remote_copy_list) == [(aiida_localhost.uuid, str(tmp_path / '*'), '.')]
 
 
+def test_nodes_remote_data_filename(generate_calc_job, generate_code, tmp_path, aiida_localhost):
+    """Test the ``nodes`` and ``filenames`` inputs with ``RemoteData`` nodes."""
+    remote_path_a = tmp_path / 'remote_a'
+    remote_path_b = tmp_path / 'remote_b'
+    remote_path_a.mkdir()
+    remote_path_b.mkdir()
+    (remote_path_a / 'file_a.txt').write_text('content a')
+    (remote_path_b / 'file_b.txt').write_text('content b')
+    remote_data_a = RemoteData(remote_path=str(remote_path_a.absolute()), computer=aiida_localhost)
+    remote_data_b = RemoteData(remote_path=str(remote_path_b.absolute()), computer=aiida_localhost)
+
+    inputs = {
+        'code': generate_code(),
+        'arguments': ['{remote_a}'],
+        'nodes': {
+            'remote_a': remote_data_a,
+            'remote_b': remote_data_b,
+        },
+        'filenames': {'remote_a': 'target_remote'},
+    }
+    dirpath, calc_info = generate_calc_job('core.shell', inputs)
+
+    code_info = calc_info.codes_info[0]
+    assert code_info.cmdline_params == ['target_remote']
+
+    assert calc_info.remote_symlink_list == []
+    assert sorted(calc_info.remote_copy_list) == [
+        (aiida_localhost.uuid, str(remote_path_a), 'target_remote'),
+        (aiida_localhost.uuid, str(remote_path_b / '*'), '.'),
+    ]
+    assert sorted(p.name for p in dirpath.iterdir()) == []
+
+
 def test_nodes_base_types(generate_calc_job, generate_code):
     """Test the ``nodes`` input with ``BaseType`` nodes ."""
     inputs = {
diff --git a/tests/conftest.py b/tests/conftest.py
index 76190db..46a8ac0 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -58,7 +58,7 @@ def factory(entry_point_name='core.shell', store_provenance=False, filepath_retr
 
 
 @pytest.fixture
-def generate_calc_job(tmp_path):
+def generate_calc_job(tmp_path_factory):
     """Create a :class:`aiida.engine.CalcJob` instance with the given inputs.
 
     The fixture will call ``prepare_for_submission`` and return a tuple of the temporary folder that was passed to it,
@@ -81,6 +81,7 @@ def factory(
             which ensures that all input files are written, including those by the scheduler plugin, such as the
             submission script.
         """
+        tmp_path = tmp_path_factory.mktemp('calc_job_submit_dir')
         manager = get_manager()
         runner = manager.get_runner()
 
diff --git a/tests/test_launch.py b/tests/test_launch.py
index 5a1edb2..dfbe236 100644
--- a/tests/test_launch.py
+++ b/tests/test_launch.py
@@ -164,6 +164,28 @@ def test_nodes_remote_data(tmp_path, aiida_localhost, use_symlinks):
     assert (dirpath_working / 'filled' / 'file_b.txt').read_text() == 'content b'
 
 
+def test_nodes_remote_data_filename(tmp_path_factory, aiida_localhost):
+    """Test copying contents of a ``RemoteData`` to specific subdirectory."""
+    dirpath_remote = tmp_path_factory.mktemp('remote')
+    dirpath_source = dirpath_remote / 'source'
+    dirpath_source.mkdir()
+    (dirpath_source / 'file.txt').touch()
+    remote_data = RemoteData(remote_path=str(dirpath_remote), computer=aiida_localhost)
+
+    results, node = launch_shell_job(
+        'echo',
+        arguments=['{remote}'],
+        nodes={'remote': remote_data},
+        filenames={'remote': 'sub_directory'},
+    )
+    assert node.is_finished_ok
+    assert results['stdout'].get_content().strip() == 'sub_directory'
+    dirpath_working = pathlib.Path(node.outputs.remote_folder.get_remote_path())
+    assert (dirpath_working / 'sub_directory').is_dir()
+    assert (dirpath_working / 'sub_directory' / 'source').is_dir()
+    assert (dirpath_working / 'sub_directory' / 'source' / 'file.txt').is_file()
+
+
 def test_nodes_base_types():
     """Test a shellfunction that specifies positional CLI arguments that are interpolated by the ``kwargs``."""
     nodes = {