U-Pb zircon and monazite ages from the oldest and youngest granite phases of the composite Stinkbank pluton in the south Central Zone of the Pan-African Damara belt in Namibia indicate a timing of emplacement of the composite pluton between 547.5 ± 4.7 Ma and 529.4 ± 4 Ma. This documents the assembly of the sheet-like pluton over a period of 17 ± 7 Ma (2σ ) in the lower Cambrian. Intrusive relationships, the folding of all granite phases and the pervasive development of magmatic and solid-state foliations indicate the syn-tectonic emplacement and deformation of the pluton during northwest-southeast shortening (D3) over a protracted time between >550 Ma and <530 Ma. On a regional scale, D3 shortening strains related to the high-angle convergence between the Kalahari and Congo Cratons can be recorded over a period of >50 Ma in the south Central Zone, between >560 Ma and at least 500 Ma. We suggest that previously identified deformation episodes do not represent distinct deformational phases related to changes in regional stress fields or plate kinematics. Instead, different kinematics and the seemingly different timing of deformational episodes are the result of variations of the strength of the Central Zone during high-angle convergence. Mid- and lower-crustal levels are decoupled from the upper crust, forming a ductile, partially molten orogenic infrastructure beneath a rheologically stronger, upper-crustal superstructure. Variations in crustal rheologies are brought about by regional high-T metamorphism and, in particular, partial melting of mid- and lower crustal levels. The presence of melts and advective heat transport through granite plutons has resulted in a similar weakening of even upper crustal levels, although spatially restricted to the intrusions and immediate wall rocks. The orogenic superstructure-infrastructure also implies that the correlation of deformational events through seemingly syn-, late- and post-tectonic granite intrusions from different parts and levels of the orogen may lead to erroneous interpretations of the actual timing of events.