Fire has been an integral part of ecosystem functioning in many biomes for a long time, but the increased intensity and frequency of wildfires often affect plant diversity and carbon storage. Prescribed burning is one of the alternatives to forest fuel management where the fire is controlled and carried out under a determined set of weather conditions and objectives. The effect of prescribed burning on plant diversity and carbon (C) storage has not been studied widely. The objective of this study was to evaluate the effect of prescribed burning on plant diversity indices, biomass stocks, and soil C storage in the tropical highland forests of Southern Mexico. We assessed plant diversity and carbon stocks at 21 sampling sites: seven with prescribed burning, seven non-burning, and seven with wildfires. We calculated tree biodiversity indices, stand structural properties, and species composition among burning treatments. We quantified C stocks in vegetation biomass by using an allometric equation and forest litter by direct sampling. We analyzed 252 soil samples for soil organic C content and other properties. The results showed that the biodiversity index was higher in sites with prescribed burning (Shannon index, H = 1.26) and non-burning (H = 1.14) than in wildfire sites (H = 0.36). There was a greater similarity in plant species composition between non-burning and prescribed burning sites compared to wildfire sites. Prescribed burning showed a positive effect on soil carbon storage (183.9 Mg C ha−1) when compared to wildfire (144.3 Mg C ha−1), but the difference was not statistically significant (p > 0.05) in biomass stocks. Prescribed burning in this study conserved plant diversity as well as soil carbon stocks compared to non-burning, the opposite of what we found in wildfires.