Device structures for a bipolar junction transistor and methods for fabricating a device structure using a substrate. One or more primary trench isolation regions are formed that surround an active device region of the substrate and a collector contact region of the substrate. A base layer is formed on the active device region and the collector contact region, and the active device region includes a collector. Each primary trench isolation region extends vertically to a first depth into the substrate. A trench is formed laterally located between the base layer and the collector contact region and that extends vertically through the base layer and into the substrate to a second depth that is less than the first depth. A dielectric is formed in the trench to form a secondary trench isolation region. An emitter is formed on the base layer.