diff --git a/janus_core/calculations/md.py b/janus_core/calculations/md.py
index d3ea513f..006bce4c 100644
--- a/janus_core/calculations/md.py
+++ b/janus_core/calculations/md.py
@@ -808,7 +808,18 @@ def _prepare_restart(self) -> None:
             restart_stem = self._restart_stem
 
             # Use restart_stem.name otherwise T300.0 etc. counts as extension
-            poss_restarts = restart_stem.parent.glob(f"{restart_stem.name}*.extxyz")
+            poss_restarts = list(
+                restart_stem.parent.glob(f"{restart_stem.name}*.extxyz")
+            )
+
+            # If no restarts found, check potential last results directory
+            if not poss_restarts:
+                results_dirs = sorted(restart_stem.parent.parent.glob("janus_results*"))
+                if results_dirs:
+                    poss_restarts = results_dirs[-1].glob(
+                        f"{restart_stem.name}*.extxyz"
+                    )
+
             try:
                 last_restart = max(poss_restarts, key=getmtime)
 
diff --git a/janus_core/helpers/utils.py b/janus_core/helpers/utils.py
index 41456b64..432d714c 100644
--- a/janus_core/helpers/utils.py
+++ b/janus_core/helpers/utils.py
@@ -7,6 +7,7 @@
 from io import StringIO
 from logging import Logger
 from pathlib import Path
+import re
 from typing import Any, Literal, TextIO
 
 from ase import Atoms
@@ -110,8 +111,23 @@ def _get_default_prefix(
             struct_name = struct.get_chemical_formula()
 
         # Set default output directory
-        prefix = Path("./janus_results") / struct_name
+        results_dir = Path("./janus_results")
+        results_dirs = Path(".").glob("janus_results_*")
+
+        if results_dirs:
+            idx = (
+                int(match.group(0))
+                for dir in results_dirs
+                if (match := re.search("([0-9]+)$", str(dir)))
+            )
+            new_idx = max(idx, default=-1) + 1
+
+            if new_idx:
+                results_dir = Path(f"./janus_results_{new_idx}")
+            elif results_dir.exists():
+                results_dir = Path("./janus_results_1")
 
+        prefix = results_dir / struct_name
         return "-".join((str(prefix), *filter(None, additional)))
 
     def _build_filename(
diff --git a/tests/test_filenamemixin.py b/tests/test_filenamemixin.py
index c3a01955..02ccbabd 100644
--- a/tests/test_filenamemixin.py
+++ b/tests/test_filenamemixin.py
@@ -8,6 +8,7 @@
 import pytest
 
 from janus_core.helpers.utils import FileNameMixin
+from tests.utils import chdir
 
 DATA_PATH = Path(__file__).parent / "data"
 STRUCT = read(DATA_PATH / "benzene.xyz")
@@ -125,3 +126,35 @@ def test_file_name_mixin_build(mixin_params, file_args, file_kwargs, file_name):
     assert (
         file_mix.build_filename(*file_args, **file_kwargs) == Path(file_name).absolute()
     )
+
+
+@pytest.mark.parametrize(
+    "existing_dirs, expected_new_dir",
+    (
+        ((), "janus_results"),
+        (("janus_results",), "janus_results_1"),
+        (("janus_results", "janus_results_1"), "janus_results_2"),
+        (("janus_results", "janus_results_1", "janus_results_2"), "janus_results_3"),
+        # Check non-sequential output directories
+        (("janus_results_1",), "janus_results_2"),
+        (("janus_results_2",), "janus_results_3"),
+        (("janus_results_1", "janus_results_2"), "janus_results_3"),
+        (("janus_results", "janus_results_2"), "janus_results_3"),
+        # Check non-default output directories
+        (("janus_results1"), "janus_results"),
+        (("janus_results", "janus_results1"), "janus_results_1"),
+        (("janus_result"), "janus_results"),
+        (("janus_results_abc"), "janus_results"),
+    ),
+)
+def test_new_results_dir(tmp_path, existing_dirs, expected_new_dir):
+    """Test the creation of new results directories."""
+    with chdir(tmp_path):
+        for dir in existing_dirs:
+            Path(dir).mkdir(parents=True, exist_ok=True)
+
+        file_mix = DummyFileHandler(STRUCT, None, None)
+        assert (
+            file_mix.file_prefix.as_posix()
+            == (Path(expected_new_dir) / "C6H6").as_posix()
+        )