Yes, the GlacioTex Cooling Cover will definitely still work well when used with a mattress protector. The GlacioTex fabric is sewn into the surface of your mattress and works in two ways to keep you cool: by providing a cool-to-the-touch finish on the surface of the mattress and by relying on fibers with high thermal conductivity to push heat away from your body while you sleep. An additional layer, like the Mattress Protector, will limit the cool-to-the touch surface a bit but you will certainly still benefit from dispersed heat away from your body so you can enjoy a cool night's sleep.