Mangrove forests are increasingly threatened by selective deforestation, yet understanding of the implications of different modes of deforestation for the functioning of these ecosystems is limited. Benthic macroinfaunal communities are integral components of mangrove ecosystems, supporting biogeochemical cycling and providing food to higher trophic levels, but their response to selective deforestation is unknown. Macroinfaunal community structure, biodiversity, and functioning were compared among 4 estuarine mangrove systems exposed to varying degrees of deforestation along the coast of Ghana. At higher tidal elevations, biomass, bioturbation potential, and secondary production estimates were significantly larger in the intact mangroves compared to selectively deforested and clear-felled sites. Differences in canopy cover were important in explaining the significant differences in macroinfaunal community composition between the intact and selectively deforested sites. Biological traits analysis showed that macroinfaunal assemblages were distinct between the intact and deforested mangroves, with deforested areas exhibiting reduced trait diversity. Both modes of mangrove deforestation degraded ecosystem functioning through their impact upon macroinfaunal communities. In clear-felled mangroves, secondary production and bioturbation potential were reduced by 94 and 90%, respectively, while in selectively deforested mangroves, both metrics were reduced by 98% compared to intact mangroves. This case study provides clear evidence that both clear-felling and selective mangrove deforestation can have a significant impact on benthic macroinfaunal communities and their functioning.