As part of a project ordered by the Ministry of Science, Technology and Innovation of Brazil, an assessment of Brazilian biological collections was conducted by the Brazilian Societies of Botany, Microbiology, Virology and Zoology to obtain data on the current state of these collections. The goal was to provide subsidies for future public policies, including financial support and prioritization policies. Herein, we present the results of the microbiological collections, which play a fundamental role in the ex situ conservation of biodiversity and support research, development and innovation. A survey was sent to public and private institutions in Brazil and answered by 168 microbiological collections from 79 different institutions. Among these, 73 comprise public research institutions and universities, demonstrating the State's importance in preserving and safeguarding Brazilian microbial diversity. The main taxonomic groups are bacteria (present in 70.24% of the collections) and fungi (52.98% of the collections) from different Brazilian ecosystems and biomes, including several type strains. Furthermore, the collections preserve microorganisms with biotechnological potential for application in environmental protection, public health, industry, and agribusiness. However, despite all these economic and biotechnological potentials, the data analysis showed serious limitations and fragilities, especially regarding physical infrastructure and human resources, and raises alerts about the risk that Brazilian collections are subjected to.