An imaging pixel may include an upper substrate layer with a photosensitive layer and a lower substrate with a photosensitive layer. A color filter layer may be formed over the upper substrate layer. The color filter layer may include a color filter window that allows light to pass through the upper substrate layer to the photosensitive layer in the lower substrate. The color filter window may be formed from a dielectric material or from a color filter element with a different color than the surrounding color filter element. A metal interconnect layer may couple the lower substrate layer to the upper substrate layer. The color filter window may be formed in the central portion of a pixel, or between multiple pixels in an image sensor.