A method of manufacturing a semiconductor device includes forming an active region on a substrate, forming a gate structure on the substrate intersecting the active region, removing an upper portion of the gate structure and forming a gate capping layer, forming a preliminary contact plug electrically connected to a portion of the active region, the preliminary contact plug including first and second portions, forming a mask pattern layer including a first pattern layer covering an upper surface of the gate capping layer, and a second pattern layer extending from the first pattern layer to cover the second portion of the preliminary contact plug, and forming a contact plug using the mask pattern layer as an etch mask by recessing the first portion of the preliminary contact plug exposed by the mask pattern layer to a predetermined depth from an upper surface of the preliminary contact plug.