diff --git a/src/batdetect2/cli/train.py b/src/batdetect2/cli/train.py
index 8a6c8ef..e169e3e 100644
--- a/src/batdetect2/cli/train.py
+++ b/src/batdetect2/cli/train.py
@@ -24,6 +24,14 @@ __all__ = ["train_command"]
         "training starts from a fresh model config."
     ),
 )
+@click.option(
+    "--base-dir",
+    type=click.Path(exists=True),
+    help=(
+        "Base directory used to resolve relative paths inside the training "
+        "and validation dataset configs."
+    ),
+)
 @click.option(
     "--targets",
     "targets_config",
@@ -111,6 +119,7 @@ def train_command(
     model_path: Path | None = None,
     ckpt_dir: Path | None = None,
     log_dir: Path | None = None,
+    base_dir: Path | None = None,
     targets_config: Path | None = None,
     model_config: Path | None = None,
     training_config: Path | None = None,
@@ -191,7 +200,10 @@ def train_command(
         model_conf = model_conf.model_copy(update={"targets": target_conf})
 
     logger.info("Loading training dataset...")
-    train_annotations = load_dataset_from_config(train_dataset)
+    train_annotations = load_dataset_from_config(
+        train_dataset,
+        base_dir=base_dir,
+    )
     logger.debug(
         "Loaded {num_annotations} training examples",
         num_annotations=len(train_annotations),
@@ -199,7 +211,10 @@ def train_command(
 
     val_annotations = None
     if val_dataset is not None:
-        val_annotations = load_dataset_from_config(val_dataset)
+        val_annotations = load_dataset_from_config(
+            val_dataset,
+            base_dir=base_dir,
+        )
         logger.debug(
             "Loaded {num_annotations} validation examples",
             num_annotations=len(val_annotations),