As part of the REgional Carbon Cycle Assessment and Processes Phase 2 (RECCAP2) project, we developed a comprehensive African Greenhouse gases (GHG) budget covering 2000 to 2019 (RECCAP1 and RECCAP2 time periods), and assessed uncertainties and trends over time. We compared bottom-up process-based models, data-driven remotely sensed products, and national GHG inventories with top-down atmospheric inversions, accounting also for lateral fluxes. We incorporated emission estimates derived from novel methodologies for termites, herbivores, and fire, which are particularly important in Africa. We further constrained global woody biomass change products with high-quality regional observations. During the RECCAP2 period, Africa's carbon sink capacity is decreasing, with net ecosystem exchange switching from a small sink of −0.61 ± 0.58 PgC yr⁻¹ in RECCAP1 to a small source in RECCAP2 at 0.16 (−0.52/1.36) PgC yr⁻¹. Net CO2 emissions estimated from bottom-up approaches were 1.6 (−0.9/5.8) PgCO2 yr⁻¹, net CH4 were 77 (56.4/93.9) TgCH4 yr⁻¹ and net N2O were 2.9 (1.4/4.9) TgN2O yr⁻¹. Top-down atmospheric inversions showed similar trends. Land Use Change emissions increased, representing one of the largest contributions at 1.7 (0.8/2.7) PgCO2eq yr⁻¹ to the African GHG budget and almost similar to emissions from fossil fuels at 1.74 (1.53/1.96) PgCO2eq yr⁻¹, which also increased from RECCAP1. Additionally, wildfire emissions decreased, while fuelwood burning increased. For most component fluxes, uncertainty is large, highlighting the need for increased efforts to address Africa-specific data gaps. However, for RECCAP2, we improved our overall understanding of many of the important components of the African GHG budget that will assist to inform climate policy and action.