This study integrates LA-ICP-MS zircon U–Pb ages and the first zircon trace element data from metasedimentary and metaigneous rocks of the Nyong Complex (NyC) in the NW Congo Craton, southern Cameroon, to constrain its petrogenesis, tectonic setting, and crustal evolution. Chondrite-normalized REE patterns show strong HREE enrichment, depleted LREE–MREE, and pronounced positive Ce and negative Eu anomalies, indicating a magmatic origin for the zircons. Trace element signatures suggest that the zircons derived from continental crustal magmas generated under variable oxidation conditions in a long-lived arc-related tectonic environment. Detrital zircon ages range from Archean to Paleoproterozoic, with five major age peaks at 2885 ± 8 Ma, 2775 ± 6 Ma, 2654 ± 7 Ma, 2469 ± 11 Ma, and 2316 ± 11 Ma. These ages correspond to major magmatic and metamorphic events recognized in both the Congo and São Francisco cratons. The preservation of felsic continental crust between 2.9 and 2.2 Ga in the NyC and the Borborema Province (NE Brazil) likely records a critical transition in Earth’s geodynamic regime, marked by enhanced consumption and recycling of mafic crust during Proterozoic accretion compared to the late Archean. This transition reflects the onset of modern-style plate tectonics, enabling craton stabilization and contributing to the assembly of the Nuna/Columbia supercontinent. The NyC is thus interpreted as part of the Trans-Amazonian belt, analogous to that in NE Brazil, and formed during the collision between the Congo and São Francisco cratons.