diff --git a/lib/standard/runners/genignore.rb b/lib/standard/runners/genignore.rb
index 74236749..e6556f49 100644
--- a/lib/standard/runners/genignore.rb
+++ b/lib/standard/runners/genignore.rb
@@ -13,6 +13,7 @@ def call(config)
           config.rubocop_options[:formatters] = [["files", temp_file.path]]
           config.rubocop_options[:format] = "files"
           config.rubocop_options[:out] = temp_file.path
+          remove_project_files_from_ignore_list(config)
           Runners::Rubocop.new.call(config)
 
           # Read in the files with errors.  It will have the absolute paths
@@ -43,6 +44,14 @@ def call(config)
           temp_file.unlink
         end
       end
+
+      # FIXME: This will also remove files which are in
+      # `Standard::CreatesConfigStore::ConfiguresIgnoredPaths::DEFAULT_IGNORES`.
+      def remove_project_files_from_ignore_list(config)
+        options_config = config.rubocop_config_store.instance_variable_get("@options_config")
+        options_config["AllCops"] ||= []
+        options_config["AllCops"]["Exclude"] = []
+      end
     end
   end
 end
diff --git a/test/standard/runners/genignore_test.rb b/test/standard/runners/genignore_test.rb
index 407634fa..49527ef6 100644
--- a/test/standard/runners/genignore_test.rb
+++ b/test/standard/runners/genignore_test.rb
@@ -30,6 +30,17 @@ def test_todo_generated
   def create_config(config_path)
     store = RuboCop::ConfigStore.new.tap do |config_store|
       config_store.options_config = config_path
+
+      # Simulate a `.standard_todo.yml` that contains an ignore file:
+      #
+      #   ---
+      #   ignore:
+      #     - errors_one.rb
+      #
+      options_config = config_store.instance_variable_get("@options_config")
+      options_config["AllCops"] ||= []
+      options_config["AllCops"]["Exclude"] ||= []
+      options_config["AllCops"]["Exclude"] |= [path("errors_one.rb")]
     end
 
     Standard::Config.new(nil, ["."], {}, store)