Soy [Glycine max (L.) Merrill] and corn (Zea mays L.) are important crops in Brazilian agribusiness. When stored improperly, these grains are susceptible to insects and microorganisms. Among the microorganisms capable of causing grain deterioration, fungi stand out. Despite the harm associated with fungi, they are biotechnologically appreciable due to their potential ability to produce hydrolytic enzymes, such as cellulases and proteases. Fungal hydrolytic enzymes have been applied in various processes in the food, textile, and detergent production industries, among others. The objective of this study was to verify the presence of fungi in samples of corn and soybean grains under storage conditions and characterize them regarding the production of cellulolytic and proteolytic enzymes. Among the results, there was a greater quantity and variety of filamentous fungi (35 morphotypes) in association with the grains evaluated, than of yeasts (three morphotypes). Representatives of the genera Aspergillus spp., Curvularia sp., and Penicillium spp. were detected, corroborating previous reports in the literature. Filamentous fungi that tested positive for cellulase production had an enzyme ratio index (ERI) varying between 1.06 and 2.57 (mean ± standard deviation = 1.37 ± 0.48), while for proteolytic activity, only the fungi isolated from soybean tested positive, with ERI (mean ± standard deviation) = 1.21 ± 0.01. Although the taxonomy of the isolates in this study has not been completely elucidated, it is possible to state that these fungi are promising for producing hydrolytic enzymes, with potential for use in the development of products and/or biotechnological processes.