Ganoderma lucidum's potential to decolorize and detoxify malachite green (MG) was studied. A Plackett-Burman experimental design to select operational factors and conditions favoring decolorization associated with laccase activity was performed. The most influential variables based on this statistical optimization were temperature, rpm for flask agitation, inoculum percentage, and dye concentration. Based on these features, removal experiments for 96 h were performed. Following thr 96-h removal assays, it was demonstrated that viable biomass at different glucose concentrations was able to remove over 90% MG at a 10 mg/L concentration, evidencing a positive correlation with laccase activity. Adsoprtion studies allowed to evidence acid pHs favored MG adsorption, with the Elovich model best describing the chimioadsorption phenomenon. Finally, it was demonstrated that MG (10 mgL−1) without treatment was highly toxic for Lactuca sativa seed germination index (GI) (<50%). This index increased when seeds were exposed to MG solution after it was treated with G. lucidum viable biomass (VB).