Shrimp farms are blooming around the world and, despite generating protein supply, employment, and income for the human population, they also represent one of the main threats to mangroves, biodiversity hotspots, and providers of multiple ecosystem goods and services. Despite several studies reporting the impact of carcinoculture on marine biota, the effects promoted on the structure and functioning of microbial communities, as well as on the ecosystem services offered, still represent knowledge gaps. Likewise, the recovery capacity of these microbiomes in response to mangrove forest recolonization is also an unanswered question.