diff --git a/lib/jekyll/plugin_manager.rb b/lib/jekyll/plugin_manager.rb
index 13b554a4..5ba0924f 100644
--- a/lib/jekyll/plugin_manager.rb
+++ b/lib/jekyll/plugin_manager.rb
@@ -90,8 +90,8 @@ module Jekyll
     end
 
     def deprecation_checks
-      pagination_included =  (!(site.config['gems'] || []).include?('jekyll-paginate') || !defined?(Jekyll::Paginate))
-      if site.config['paginate'] && pagination_included
+      pagination_included = (site.config['gems'] || []).include?('jekyll-paginate') || defined?(Jekyll::Paginate)
+      if site.config['paginate'] && !pagination_included
         Jekyll::Deprecator.deprecation_message "You appear to have pagination " +
           "turned on, but you haven't included the `jekyll-paginate` gem. " +
           "Ensure you have `gems: [jekyll-paginate]` in your configuration file."