The Forest Stewardship Council (FSC) forest certification was introduced in Nepal with an assumption that it improves forests and ecosystem services while addressing the drivers of forest degradation. As of today, 89 community forests (CF) have been FSC certified, however empirical evidence on the contribution of forest certification on carbon stock and species richness is lacking. This research, thus tries to answer the question “do certified community forests (CCF) maintain higher carbon stock and species richness compared to non-certified community forests (NCF)?” The study collected field level data during February–May 2013 from 88 experimental plots. The study found higher carbon stock (p<0.05) and species richness, and lower ecological threat index (p<0.10) in the CCF, compared to NCF. The study showed that forest carbon stock is positively related to species richness, and negatively to ecological threat index. It suggests that sustainable forest management practices, that is generally adopted in the CCF, would minimize ecological threats, enriches species leading to enhanced carbon stock.