Central African great ape populations are in serious decline as a result of poaching, habitat loss and disease. Reliable estimates of population size are urgently needed for informed management action. We estimate the abundance and distribution of central chimpanzee Pan troglodytes troglodytes and western lowland gorilla Gorilla gorilla gorilla populations in the c. 11,000 km2 Dja-Ngoyla Complex in Cameroon, a critical component of the Tri National Dja-Odzala-Minkébé (TRIDOM) transboundary landscape, which covers 178,000 km2. We compare our results with previous site estimates and with other population estimates from the region. We completed 1,096.64 km of line transects (n = 559) in 2021 using the standing-crop nest counts method. The Dja-Ngoyla Complex supported c. 11,787 great apes. Chimpanzee abundance was significantly higher in Dja, and Ngoyla-Mintom supported 71% of the gorilla population. Thirty-seven per cent of the gorilla population and 17% of the chimpanzee population occurred in logging concessions. There was no significant change in the species’ abundance in Dja Faunal Reserve compared to our 2018 estimate using the same methodology. The chimpanzee population density was much higher in Dja and Ngoyla Faunal Reserves compared to other protected areas in the region. There was large variation in great ape densities across logging concessions, and those with implemented management certification schemes supported higher densities. This study also highlights the high risk of Dja’s great ape population becoming isolated. Promoting forest management certification to strengthen wildlife and habitat protection in all logging concessions in the Complex is urgently needed and will also allow local communities to benefit from these forests.