Calderas are formed by the collapse of large magma reservoirs and are commonly elliptical in map view. The orientation of elliptical calderas is often used as an indicator of the local stress regime; but, in some rift settings, pre-existing structural trends may also influence the orientation. We investigated whether either of these two mechanisms controls the orientation of calderas in the Kenyan Rift. Satellite-based mapping was used to identify the rift border faults, intra-rift faults and orientation of the calderas to measure the stress orientations and pre-existing structural trends and to determine the extensional regime at each volcano. We found that extension in northern Kenya is orthogonal, whereas that in southern Kenya is oblique. Elliptical calderas in northern Kenya are orientated NW–SE, aligned with pre-existing structures and perpendicular to recent rift faults. In southern Kenya, the calderas are aligned NE–SW and lie oblique to recent rift faults, but are aligned with pre-existing structures. We conclude that, in oblique continental rifts, pre-existing structures control the development of elongated magma reservoirs. Our results highlight the structural control of magmatism at different crustal levels, where pre-existing structures control the storage and orientation of deeper magma reservoirs and the local stress regime controls intra-rift faulting and shallow magmatism.