Tropical forests play an important role in mitigating global climate change, emphasizing the need for reliable estimates of forest carbon stocks at regional and global scales. This is essential for effective carbon management, which involves strategies like emission reduction and enhanced carbon sequestration through forest restoration and conservation. However, reliable sample-based estimations of forest carbon stocks require accurate allometric equations, which are lacking for the rainforests of the Atlantic Forest Domain (AFD). In this study, we fitted biomass equations for the three main AFD forest types and accurately estimated the amount of carbon stored in their above-ground biomass (AGB) in Rio de Janeiro state, Brazil. Using non-destructive methods, we measured the total wood volume and wood density of 172 trees from the most abundant species in the main remnants of rainforest, semideciduous forest, and restinga forest in the state. The biomass and carbon stocks were estimated with tree-level data from 185 plots obtained in the National Forest Inventory conducted in Rio de Janeiro. Our locally developed allometric equations estimated the state’s biomass stocks at 70.8 ± 5.4 Mg ha−1 and carbon stocks at 35.4 ± 2.7 Mg ha−1. Notably, our estimates were more accurate than those obtained using a widely applied pantropical allometric equation from the literature, which tended to overestimate biomass and carbon stocks. These findings can be used for establishing a baseline for monitoring carbon stocks in the Atlantic Forest, especially in the context of the growing voluntary carbon market, which demands more consistent and accurate carbon stock estimations.