Anthropogenic activities such as mining and agriculture are the main ones responsible for increasing environmental contamination with heavy metals and highly toxic agrochemicals respectively. In recent decades, the use of microorganisms as alternatives to clean contaminated environments has been explored. Specifically, fungi have emerged as powerful agents used in the bioremediation of contaminated sites, demonstrating their efficiency in mitigating the impact of diverse contaminants on ecosystems. This Chapter discusses in depth the diverse mechanisms employed by fungi to clean contaminated environments with heavy metals or toxic agrochemicals. Highlighting the remarkable abilities of fungi for metal hyperaccumulation, degradation of agrochemicals, and their potential contributions as biotechnological tools to sustainable environmental solutions of highly contaminated sites.