Marine carbonate sediments have economic value because of their high concentration of calcium minerals and important trace elements. However, increasing mining interest in these stocks is threatening unique ecosystems, such as rhodolith beds, which provide many ecosystem goods and services. We review the potential of the unexplored Brazilian deposits and the rising conflicts with other blue economic sectors and biodiversity hotspots. The tropical Southwestern Atlantic Ocean, particularly the Brazilian Exclusive Economic Zone, has the largest deposit of marine limestone worldwide, which is very attractive to the global industry, with reserves measured at more than 1355,157,240 tons of CaCO3 and it is especially useful as a supply for agriculture and animal nutrition. This large mining potential raises concerns regarding licenses and potential impacts, especially considering the biological and socio-economic importance of extensive rhodolith beds, which may conflict with mining. Additionally, future dredging activities will take place in vulnerable ecosystems without adequate marine spatial planning (MSP). Currently, there is no long-term scientific information on the available carbonate stocks, stock recoverability, risks to connectivity with other ecosystems (e.g., coral reefs), and the reduced provision of ecosystem services which may affect activities such as artisanal fisheries. In this context, encouraging carbonate mining without science-based information and MSP accelerates the unsustainable exploitation of this important ecosystem. This activity will contribute to the degradation of tropical marine biodiversity and threaten the food security of traditional and vulnerable human communities, which is in opposition to the Sustainable Development Goals and reaching the 2030 United Nations Agenda.