In rifts the structural evolution of calderas helps to characterize the spatiotemporal relationships between magmatism, long wavelength crustal deformation and the formation of tectonic deformation zones along the rift axis. We document the structural characteristics of the ∼36 ka old Menengai Caldera, situated within a young zone of extension of the central Kenya Rift. Field mapping and high-resolution digital surface models reveal that NNE-striking Holocene normal faults perpendicular to the regional ESE-WNW extension direction dominate the interior sectors of the rift. Inside the caldera, structures are overprinted by post-collapse doming and faulting of the magmatic centre, resulting in obliquely slipping normal faults bounding a resurgence horst. Radiocarbon dating of faulted units as young as 5 ka cal BP and palaeo-shorelines of a lake formed during the African Humid Period in the Nakuru Basin indicate that volcanism and fault activity inside and in the vicinity of Menengai must have been sustained during the Holocene. Our analysis confirms that the caldera is located at the centre of an extending rift segment, and suggests that other magmatic centres and young zones of faulting along the volcano-tectonic axis of the Kenya Rift may constitute nucleation points of faulting that ultimately foster future continental break-up.