diff --git a/lib/autoproj/cli/update.rb b/lib/autoproj/cli/update.rb
index 6c0b9eed..b8c83f63 100644
--- a/lib/autoproj/cli/update.rb
+++ b/lib/autoproj/cli/update.rb
@@ -97,6 +97,8 @@ def run(selected_packages, run_hook: false, **options)
                     command_line_selection, selected_packages =
                         finish_loading_configuration(selected_packages)
                 else
+                    ws.setup_all_package_directories
+                    ws.finalize_package_setup
                     command_line_selection, selected_packages = [], PackageSelection.new
                 end
 
diff --git a/test/cli/test_update.rb b/test/cli/test_update.rb
index 7449aadc..7a7015eb 100644
--- a/test/cli/test_update.rb
+++ b/test/cli/test_update.rb
@@ -196,6 +196,13 @@ module CLI
                         with(hsh(checkout_only: true)).once
                     cli.run([], checkout_only: true)
                 end
+                it "properly sets up packages while updating configuration only" do
+                    flexmock(ws).should_receive(:setup_all_package_directories).
+                        ordered.once
+                    flexmock(ws).should_receive(:finalize_package_setup).
+                        ordered.once
+                    cli.run([], config: true)
+                end
                 it "passes options to the osdep installer for package import" do
                     flexmock(Ops::Import).new_instances.
                         should_receive(:import_packages).