The present disclosure relates to a solid-state imaging device, an electronic apparatus, and a manufacturing method that are designed to further increase conversion efficiency. A solid-state imaging device includes a pixel in which element separation is realized by a first trench element separation region having a trench structure in a region between an FD unit and an amplifying transistor among element separation elements separating the elements constituting the pixel from one another, and a second trench element separation region having a trench structure in a region other than the region between the FD unit and the amplifying transistor among the element separation regions separating the elements constituting the pixel from one another, and the first trench element separation region is deeper than the second trench element separation region. The present technology can be applied to CMOS image sensors, for example.