A first portion of a semiconductor substrate belonging to a flash memory device region is recessed to a recess depth to form a recessed region, while a second portion of the semiconductor substrate belonging to a logic device region is protected with a masking layer. A first gate dielectric layer and a first gate conductor layer formed within the recessed region such that the first gate conductive layer is substantially coplanar with the top surfaces of the shallow trench isolation structures. A second gate dielectric layer, a second gate conductor layer, and a gate cap hard mask layer, each having a planar top surface, is subsequently patterned. The pattern of the gate structure in the flash memory device region is transferred into the first gate conductor layer and the first gate dielectric layer to form a floating gate and a first gate dielectric, respectively.