The present disclosure relates to semiconductor structures and, more particularly, to a transistor with an embedded isolation layer in a bulk substrate and methods of manufacture. The structure includes: a bulk substrate; an isolation layer embedded within the bulk substrate and below a top surface of the bulk substrate; a deep trench isolation structure extending through the bulk substrate and contacting the embedded isolation layer; and a gate structure over the top surface of the bulk substrate and vertically spaced away from the embedded isolation layer, the deep trench isolation structure and the embedded isolation layer defining an active area of the gate structure in the bulk substrate.