A semiconductor structure with dual isolation structures is disclosed. The semiconductor structure may include a protruding isolation structure in a pixel array region of a substrate and an embedded isolation structure in a peripheral device region of the same substrate. A region of the protruding isolation structure extends from an upper surface of the substrate, while another region of the protruding isolation structure may, optionally, be embedded within the substrate. The embedded isolation structure is formed within the substrate and includes an upper surface that is substantially coplanar with the upper surface of the substrate. A method of forming the semiconductor structure with dual isolation structure is also disclosed.