A method of forming a capacitive micro-electro-mechanical system (MEMS) sensor device includes at least one capacitive MEMS sensor element with at least one capacitive MEMS sensor cell. A patterned dielectric layer including a thick dielectric region and a thin dielectric region is formed on a top side of a first substrate. A second substrate is bonded to the thick dielectric region to provide at least one sealed micro-electro-mechanical system (MEMS) cavity. The second substrate is thinned to reduce a thickness of said second substrate to provide a membrane layer. Vias are etched through the membrane layer and said thick dielectric region extending into the first substrate to form embedded vias. A dielectric liner which lines the embedded vias is formed within the first substrate. The embedded vias are filed with electrically conductive TSV filler material to form a plurality of through-substrate vias (TSVs), said plurality of TSVs extending to at least a top of said membrane layer. A patterned metal cap layer including metal caps is formed on top of said plurality of TSVs. Trenches are etched through regions of the membrane layer for releasing a first portion of the membrane layer over said MEMS cavity to provide a MEMS electrode and to define a fixed electrode. A third substrate including an inner cavity and outer protruding portions framing said inner cavity is bonded to the thick dielectric. The protruding portions are bonded to the thick dielectric region and, together with said first substrate vacuum, seals said MEMS electrode. The plurality of TSVs on a bottom side of said first substrate are exposed.