The maize pathogen Fusarium verticillioides and their mycotoxins cause damage to plants, animals, and human health. This work aimed to evaluate the effect of crude extracts (CEs) from Agaricus subrufescens, Lentinula edodes, and Pleurotus ostreatus fruiting bodies on in vitro production of biomass and mycotoxins by two strains of F. verticillioides. Stipes and pilei were separated before extraction for A. subrufescens and L. edodes. Comparative metabolomics and dereplication of phenolic compounds were used to analyze all CEs. Mushroom CEs did not significantly inhibit the production of mycelial biomass at concentrations of 2 mg mL−1. CEs from A. subrufescens (stipes and pilei) and L. edodes pilei inhibited the production of fumonisins B1 + B2 + B3 by 54% to 80%, whereas CE from P. ostreatus had no effect. In contrast, CE from L. edodes stipes dramatically increased the concentration of fumonisins in culture media. Fusaric acid concentration was decreased in cultures by all CEs except L. edodes stipes. Differences in phenolic composition of the extracts may explain the different effects of the CE treatments on the production of mycotoxins. The opposing activities of stipes and pilei from L. edodes offer an opportunity to search for active compounds to control the mycotoxin production by F. verticillioides.