diff --git a/swh/fuse/cli.py b/swh/fuse/cli.py
--- a/swh/fuse/cli.py
+++ b/swh/fuse/cli.py
@@ -194,8 +194,8 @@
 
     def rm_cache(conf, cache_name):
         try:
-            conf["cache"][cache_name]["path"].unlink(missing_ok=True)
-        except KeyError:
+            Path(conf["cache"][cache_name]["path"]).unlink()
+        except (FileNotFoundError, KeyError):
             pass
 
     conf = ctx.obj["config"]
diff --git a/swh/fuse/tests/conftest.py b/swh/fuse/tests/conftest.py
--- a/swh/fuse/tests/conftest.py
+++ b/swh/fuse/tests/conftest.py
@@ -7,7 +7,6 @@
 from multiprocessing import Process
 import os
 from pathlib import Path
-import subprocess
 from tempfile import NamedTemporaryFile, TemporaryDirectory
 import time
 
@@ -32,7 +31,6 @@
 @pytest.fixture
 def fuse_mntdir(web_api_mock):
     tmpdir = TemporaryDirectory(suffix=".swh-fuse-test")
-    tmpfile = NamedTemporaryFile(suffix=".swh-fuse-test.yml")
 
     config = {
         "cache": {"metadata": {"in-memory": True}, "blob": {"in-memory": True},},
@@ -42,9 +40,9 @@
 
     # Run FUSE in foreground mode but in a separate process, so it does not
     # block execution and remains easy to kill during teardown
-    def fuse_process(tmpdir, tmpfile):
-        with tmpdir as mntdir, tmpfile as config_path:
-            config_path = Path(config_path.name)
+    def fuse_process(mntdir: Path):
+        with NamedTemporaryFile(suffix=".swh-fuse-test.yml") as tmpfile:
+            config_path = Path(tmpfile.name)
             config_path.write_text(yaml.dump(config))
             CliRunner().invoke(
                 cli.fuse,
@@ -52,12 +50,12 @@
                     "--config-file",
                     str(config_path),
                     "mount",
-                    mntdir,
+                    str(mntdir),
                     "--foreground",
                 ],
             )
 
-    fuse = Process(target=fuse_process, args=[tmpdir, tmpfile])
+    fuse = Process(target=fuse_process, args=[Path(tmpdir.name)])
     fuse.start()
     # Wait max 3 seconds for the FUSE to correctly mount
     for i in range(30):
@@ -73,5 +71,5 @@
 
     yield Path(tmpdir.name)
 
-    subprocess.run(["fusermount", "-u", tmpdir.name], check=True)
+    CliRunner().invoke(cli.umount, [tmpdir.name])
     fuse.join()
diff --git a/swh/fuse/tests/test_cli.py b/swh/fuse/tests/test_cli.py
--- a/swh/fuse/tests/test_cli.py
+++ b/swh/fuse/tests/test_cli.py
@@ -3,16 +3,35 @@
 # License: GNU General Public License version 3, or any later version
 # See top-level LICENSE file for more information
 
-import os
+from click.testing import CliRunner
+import yaml
 
-from swh.fuse.tests.data.config import REGULAR_FILE
+import swh.fuse.cli as cli
 
+# mount/umount commands are already tested when setting up the fuse_mntdir fixture
 
-def test_mountpoint(fuse_mntdir):
-    archive_dir = fuse_mntdir / "archive"
-    meta_dir = fuse_mntdir / "meta"
-    assert os.listdir(archive_dir) == []
-    assert os.listdir(meta_dir) == []
-    # On the fly mounting
-    file_path = archive_dir / REGULAR_FILE
-    assert file_path.is_file()
+
+def test_clean_command(tmp_path):
+    fake_metadata_db = tmp_path / "metadata.sqlite"
+    fake_blob_db = tmp_path / "blob.sqlite"
+    config_path = tmp_path / "config.yml"
+    config = {
+        "cache": {
+            "metadata": {"path": str(fake_metadata_db)},
+            "blob": {"path": str(fake_blob_db)},
+        },
+    }
+
+    fake_metadata_db.touch()
+    fake_blob_db.touch()
+    config_path.write_text(yaml.dump(config))
+
+    assert fake_metadata_db.exists()
+    assert fake_blob_db.exists()
+
+    CliRunner().invoke(
+        cli.fuse, args=["--config-file", str(config_path), "clean",],
+    )
+
+    assert not fake_metadata_db.exists()
+    assert not fake_blob_db.exists()
diff --git a/swh/fuse/tests/test_mountpoint.py b/swh/fuse/tests/test_mountpoint.py
new file mode 100644
--- /dev/null
+++ b/swh/fuse/tests/test_mountpoint.py
@@ -0,0 +1,22 @@
+# Copyright (C) 2020 The Software Heritage developers
+# See the AUTHORS file at the top-level directory of this distribution
+# License: GNU General Public License version 3, or any later version
+# See top-level LICENSE file for more information
+
+import os
+
+from swh.fuse.tests.data.config import ORIGIN_URL_ENCODED, REGULAR_FILE
+
+
+def test_mountpoint(fuse_mntdir):
+    assert os.listdir(fuse_mntdir) == ["archive", "meta", "origin"]
+
+
+def test_on_the_fly_mounting(fuse_mntdir):
+    assert os.listdir(fuse_mntdir / "archive") == []
+    assert os.listdir(fuse_mntdir / "meta") == []
+    assert (fuse_mntdir / "archive" / REGULAR_FILE).is_file()
+    assert (fuse_mntdir / "meta" / (REGULAR_FILE + ".json")).is_file()
+
+    assert os.listdir(fuse_mntdir / "origin") == []
+    assert (fuse_mntdir / "origin" / ORIGIN_URL_ENCODED).is_dir()