diff --git a/piptools/scripts/compile.py b/piptools/scripts/compile.py
index 37bf042b..5b14bc43 100755
--- a/piptools/scripts/compile.py
+++ b/piptools/scripts/compile.py
@@ -171,6 +171,12 @@ def cli(
         ctx.color = color
     log.verbosity = verbose - quiet
 
+    # If ``src-files` was not provided as an input, but rather as config,
+    # it will be part of the click context ``ctx``.
+    # However, if ``src_files`` is specified, then we want to use that.
+    if not src_files and ctx.default_map and "src_files" in ctx.default_map:
+        src_files = ctx.default_map["src_files"]
+
     if all_build_deps and build_deps_targets:
         raise click.BadParameter(
             "--build-deps-for has no effect when used with --all-build-deps"
diff --git a/tests/test_cli_compile.py b/tests/test_cli_compile.py
index 3341f751..f6c5be66 100644
--- a/tests/test_cli_compile.py
+++ b/tests/test_cli_compile.py
@@ -3447,6 +3447,42 @@ def test_allow_in_config_pip_sync_option(pip_conf, runner, tmp_path, make_config
     assert "Using pip-tools configuration defaults found" in out.stderr
 
 
+def test_use_src_files_from_config_if_option_is_not_specified_from_cli(
+    pip_conf, runner, tmp_path, make_config_file
+):
+    foo_in = tmp_path / "foo.in"
+    req_in = tmp_path / "requirements.in"
+
+    config_file = make_config_file("src-files", [foo_in.as_posix()])
+
+    req_in.write_text("small-fake-a==0.1", encoding="utf-8")
+    foo_in.write_text("small-fake-b==0.1", encoding="utf-8")
+
+    out = runner.invoke(cli, ["--config", config_file.as_posix()])
+
+    assert out.exit_code == 0, out
+    assert "small-fake-b" in out.stderr
+    assert "small-fake-a" not in out.stderr
+
+
+def test_use_src_files_from_cli_if_option_is_specified_in_both_config_and_cli(
+    pip_conf, runner, tmp_path, make_config_file
+):
+    foo_in = tmp_path / "foo.in"
+    req_in = tmp_path / "requirements.in"
+
+    config_file = make_config_file("src-files", [foo_in.as_posix()])
+
+    req_in.write_text("small-fake-a==0.1", encoding="utf-8")
+    foo_in.write_text("small-fake-b==0.1", encoding="utf-8")
+
+    out = runner.invoke(cli, [req_in.as_posix(), "--config", config_file.as_posix()])
+
+    assert out.exit_code == 0, out
+    assert "small-fake-a" in out.stderr
+    assert "small-fake-b" not in out.stderr
+
+
 def test_cli_boolean_flag_config_option_has_valid_context(
     pip_conf, runner, tmp_path, make_config_file
 ):