Mangroves are amongst the most productive marine ecosystems on Earth, providing a unique habitat opportunity for many species and key goods and services for human beings. Mangrove habitats are regressing at an alarming rate, due to direct anthropogenic impacts and global change. Here, in order to assess the effects of mangrove habitat degradation on benthic biodiversity and ecosystem functioning, we investigated meiofaunal biodiversity (as proxy of benthic biodiversity), benthic biomass and prokaryotic heterotrophic production (as proxies of ecosystem functioning) and trophic state in a disturbed and an undisturbed mangrove forests. We report here that disturbed mangrove area showed a loss of 20% of benthic biodiversity, with the local extinction of four Phyla (Cladocera, Kynorincha, Priapulida, Tanaidacea), a loss of 80% of microbial-mediated decomposition rates, of the benthic biomass and of the trophic resources. The results of this study strengthen the need to preserve mangrove forests and to restore those degraded to guarantee the provision of goods and services needed to support the biodiversity and functioning of wide portions of tropical ecosystems.