The rediscovery of bioactive compounds is a problem within natural product screening programs, because the chemical-genetic diversity of fungi is little explored and the standardization of cultivation conditions that allow obtaining new actives is critical in such programs. In this work, the impact of two solid mediums (rice and oats), a liquid medium (Czapeck broth) and different fermentation conditions were evaluated in order to explore new metabolic routes. Twelve filamentous fungi from Amazonian environments were used. UV-Vis spectrophotometry estimated the complexity of the extracts produced. The antimicrobial activity of the extracts was evaluated against an isolate of each Escherichia coli strain, Salmonella sp. and Staphylococcus aureus. Solid media proved to be more promising, as they allowed a wider range of active metabolites to be obtained. The oat medium provided a greater variety of metabolites, but due to the great complexity of the extracts obtained, the separation procedures were considerably more complex than for rice. Together, the rice culture medium and the use of 39 days of fermentation proved to be more promising conditions than the liquid medium normally used in screening programs in Brazil. The cultivation of Penicillium maximae (isolated for the second time in Brazilian territory) in solid medium provided the production of active fractions against E. coli in bioautography. In this study, it was observed that different fermentation conditions in solid culture are considerably promising in the search for bioactive natural products.