The main Karoo Basin (MKB) of southern Africa contains the continental record of the end-Triassic, end-Permian and end-Capitanian mass extinction events. Of these, the environmental drivers of the end-Capitanian are least known. Integrating quantitative facies analysis, provenance and geochemical data, this study investigates the rock record of end-Capitanian in the SW and S MKB and demonstrates that the previously documented biotic change coincided with a subtle variation in stratigraphic architectural styles ~260 Ma ago. Our multi-proxy sedimentological work not only defines the depositional setting of the succession as a megafan system that drained the foothills of the Cape Fold Belt, but also attempts to differentiate the tectonic and climatic controls on the fluvial architecture of this palaeontologically important Permian succession. Our results reveal persistent sediment sources, unchanged palaeocurrents, constant sandstone body geometries and possibly a constant dry palaeoclimate during the deposition of the studied interval; however, the stratigraphic trends show upward increase in: 1) laterally-accreted, sandy architectural elements; and 2) architectural elements that build the floodplain deposits. We consider this long term retrogradational stacking pattern to be linked to changes on the medial parts of southward draining megafans, where channel sinuosity increased, and depositional energy decreased at the end-Capitanian. The shift in the fluvial architecture were likely triggered by basin-wide allogenic controls rather than local autogenic processes, because this trend is observed in the coeval stratigraphic intervals from geographically disparate areas. Consequently, we propose that this regional backstepping most likely resulted from tectonic events in the adjacent Cape Fold Belt.