diff --git a/src/metatensor/models/cli/train_model.py b/src/metatensor/models/cli/train_model.py
index 62dc3a0cc..23f9a8459 100644
--- a/src/metatensor/models/cli/train_model.py
+++ b/src/metatensor/models/cli/train_model.py
@@ -109,8 +109,8 @@ def train_model(options: DictConfig) -> None:
     if not isinstance(test_options, float):
         test_options = expand_dataset_config(test_options)
         test_structures = read_structures(
-            filename=train_options["structures"]["read_from"],
-            fileformat=train_options["structures"]["file_format"],
+            filename=test_options["structures"]["read_from"],
+            fileformat=test_options["structures"]["file_format"],
         )
         test_targets = read_targets(test_options["targets"])
         test_dataset = Dataset(test_structures, test_targets)
@@ -125,8 +125,8 @@ def train_model(options: DictConfig) -> None:
     if not isinstance(validation_options, float):
         validation_options = expand_dataset_config(validation_options)
         validation_structures = read_structures(
-            filename=train_options["structures"]["read_from"],
-            fileformat=train_options["structures"]["file_format"],
+            filename=validation_options["structures"]["read_from"],
+            fileformat=validation_options["structures"]["file_format"],
         )
         validation_targets = read_targets(validation_options["targets"])
         validation_dataset = Dataset(validation_structures, validation_targets)
diff --git a/tests/cli/test_train_model.py b/tests/cli/test_train_model.py
index 06566dc0a..4aee7db5a 100644
--- a/tests/cli/test_train_model.py
+++ b/tests/cli/test_train_model.py
@@ -2,7 +2,9 @@
 import subprocess
 from pathlib import Path
 
+import ase.io
 import pytest
+from omegaconf import OmegaConf
 
 
 RESOURCES_PATH = Path(__file__).parent.resolve() / ".." / "resources"
@@ -26,6 +28,43 @@ def test_train(monkeypatch, tmp_path, output):
     assert Path(output).is_file()
 
 
+@pytest.mark.parametrize("test_set_file", (True, False))
+@pytest.mark.parametrize("validation_set_file", (True, False))
+@pytest.mark.parametrize("output", [None, "mymodel.pt"])
+def test_train_explicit_validation_test(
+    monkeypatch, tmp_path, test_set_file, validation_set_file, output
+):
+    """Test that training via the training cli runs without an error raise
+    also when the validation and test sets are provided explicitly."""
+    monkeypatch.chdir(tmp_path)
+
+    structures = ase.io.read(RESOURCES_PATH / "qm9_reduced_100.xyz", ":")
+    options = OmegaConf.load(RESOURCES_PATH / "options.yaml")
+
+    ase.io.write("qm9_reduced_100.xyz", structures[:50])
+
+    if test_set_file:
+        ase.io.write("test.xyz", structures[50:80])
+        options["validation_set"] = options["training_set"].copy()
+        options["validation_set"]["structures"]["read_from"] = "test.xyz"
+
+    if validation_set_file:
+        ase.io.write("validation.xyz", structures[80:])
+        options["test_set"] = options["training_set"].copy()
+        options["test_set"]["structures"]["read_from"] = "validation.xyz"
+
+    OmegaConf.save(config=options, f="options.yaml")
+    command = ["metatensor-models", "train", "options.yaml"]
+
+    if output is not None:
+        command += ["-o", output]
+    else:
+        output = "model.pt"
+
+    subprocess.check_call(command)
+    assert Path(output).is_file()
+
+
 def test_yml_error():
     """Test error raise of the option file is not a .yaml file."""
     try:
diff --git a/tests/resources/model.pt b/tests/resources/model.pt
deleted file mode 100644
index a8aa5a3d3..000000000
Binary files a/tests/resources/model.pt and /dev/null differ