Filamentous fungi that produce mycotoxins also demonstrate the ability to degrade a wide variety of naturally occurring and anthropogenically generated hazardous wastes. Hence, these are emerging as excellent candidates for bioremediation. Their mycelia exhibit the robustness of adapting to highly restrictive environmental conditions often experienced in the presence of persistent pollutants, which makes them more useful compared to other microbes. However, it now appears that several regulatory factors that govern mycotoxin synthesis in these toxigenic strains also regulate their bioremediation abilities. To this end, mycoremediation and mycotoxin synthesis have been thoroughly but independently investigated; hence, much less is understood about the overlaps between the two processes. This review aims to shed light on this critical knowledge gap and provide some useful insights into the future research that might overcome the challenges associated with these shared regulatory modules. This will enable the harnessing of the full potential of mycoremediation by minimizing mycotoxin contamination.