diff --git a/swh/scanner/cli.py b/swh/scanner/cli.py
--- a/swh/scanner/cli.py
+++ b/swh/scanner/cli.py
@@ -15,10 +15,8 @@
 from swh.core.cli import swh as swh_cli_group
 
 # All generic config code should reside in swh.core.config
-DEFAULT_CONFIG_PATH = os.environ.get(
-    "SWH_CONFIG_FILE", os.path.join(click.get_app_dir("swh"), "global.yml")
-)
-
+CONFIG_ENVVAR = "SWH_CONFIG_FILE"
+DEFAULT_CONFIG_PATH = os.path.join(click.get_app_dir("swh"), "global.yml")
 
 DEFAULT_CONFIG: Dict[str, Any] = {
     "web-api": {
@@ -52,15 +50,26 @@
 @click.pass_context
 def scanner(ctx, config_file: Optional[str]):
     """Software Heritage Scanner tools."""
-    if config_file is None and config.config_exists(DEFAULT_CONFIG_PATH):
-        config_file = DEFAULT_CONFIG_PATH
-
-    if config_file is None:
-        conf = DEFAULT_CONFIG
-    else:
+    env_path = os.environ.get("SWH_CONFIG_FILE")
+    def_path = DEFAULT_CONFIG_PATH
+
+    # for now assuming files do not change while running
+    if config_file and not config.config_exists(config_file):
+        raise FileNotFoundError(config_file)
+    elif env_path and not config.config_exists(env_path):
+        raise FileNotFoundError(env_path)
+    elif config_file or env_path or config.config_exists(def_path):
+        config_file = config_file or env_path or def_path
+    # config_file = (
+    #    config_file if config_file
+    #    else env_path if env_path
+    #    else def_path if config.config_exists(def_path)
+    #    else None
+    # )
+
+    conf = DEFAULT_CONFIG
+    if config_file is not None:
         # read_raw_config do not fail on ENOENT
-        if not config.config_exists(config_file):
-            raise FileNotFoundError(config_file)
         conf = config.read_raw_config(config.config_basepath(config_file))
         conf = config.merge_configs(DEFAULT_CONFIG, conf)
 
diff --git a/swh/scanner/tests/test_cli.py b/swh/scanner/tests/test_cli.py
new file mode 100644
--- /dev/null
+++ b/swh/scanner/tests/test_cli.py
@@ -0,0 +1,83 @@
+# 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
+
+from os.path import expanduser
+
+from click.testing import CliRunner
+import pytest
+
+from swh.scanner.cli import scanner
+
+
+@pytest.fixture
+def cli_runner() -> CliRunner:
+    return CliRunner()
+
+
+@pytest.fixture
+def rootpath_good() -> str:
+    return "/usr/lib/python3/dist-packages/urllib3"
+
+
+@pytest.fixture
+def rootpath_bad() -> str:
+    return "~"
+
+
+@pytest.fixture
+def confpath_good() -> str:
+    return expanduser("~/.config/swh/global.yml")
+
+
+@pytest.fixture
+def confpath_bad() -> str:
+    return "~"
+
+
+def test_smoke(cli_runner):
+    cli_runner.invoke(scanner, ["-h"])
+
+
+# TODO For nominal code paths, check that the right config file is loaded with a mock
+def test_root_path_good(cli_runner, rootpath_good):
+    # test no option no envvar no default
+    # how to make sure the default file does not exist?
+    res = cli_runner.invoke(scanner, ["scan", rootpath_good])
+    assert res.exit_code == 0
+
+
+def test_root_path_bad(cli_runner, rootpath_bad):
+    res = cli_runner.invoke(scanner, ["scan", rootpath_bad])
+    print(res.__dict__)
+    assert res.exit_code == 2
+
+
+def test_config_path_option_bad(cli_runner, confpath_bad, rootpath_good):
+    res = cli_runner.invoke(scanner, ["-C", confpath_bad, "scan", rootpath_good])
+    print(res.__dict__)
+    assert res.exception.__class__ == FileNotFoundError
+
+
+def test_config_path_envvar_good(cli_runner, confpath_good, rootpath_good, monkeypatch):
+    monkeypatch.setenv("SWH_CONFIG_FILE", confpath_good)
+    res = cli_runner.invoke(scanner, ["scan", rootpath_good])
+    assert res.exit_code == 0
+
+
+def test_config_path_envvar_bad(cli_runner, confpath_bad, rootpath_good, monkeypatch):
+    monkeypatch.setenv("SWH_CONFIG_FILE", confpath_bad)
+    res = cli_runner.invoke(scanner, ["scan", rootpath_good])
+    print(res.__dict__)
+    assert res.exception.__class__ == FileNotFoundError
+
+
+def test_config_path_option_envvar(
+    cli_runner, confpath_good, rootpath_good, monkeypatch
+):
+    monkeypatch.setenv("SWH_CONFIG_FILE", confpath_good)
+    res = cli_runner.invoke(scanner, ["-C", confpath_good, "scan", rootpath_good])
+    print(res.__dict__)
+    assert res.exit_code == 0
+    # TODO Check that option has precedence over envvar