Methods of making a logic transistor in a logic region and an NVM cell in an NVM region of a substrate include forming a conductive layer on a gate dielectric, patterning the conductive layer over the NVM region, removing the conductive layer over the logic region, forming a dielectric layer over the NVM region, forming a protective layer over the dielectric layer, removing the dielectric layer and the protective layer from the logic region, forming a high-k dielectric layer over the logic region and a remaining portion of the protective layer, and forming a first metal layer over the high-k dielectric layer. The first metal layer, the high-k dielectric, and the remaining portion of the protective layer are removed over the NVM region. A conductive layer is deposited over the remaining portions of the dielectric layer and over the first metal layer, and the conductive layer is patterned.