Oilseed plants such as cotton (Gossypium sp.) generate abundant biomass residues which contain significant levels of edible oil, crude proteins and other desirable biomolecules for the animal nutrition industry. The application of cottonseed cake in animal feed, a by-product of the cotton industry, is limited due to the natural presence of toxic free gossypol (FG), wherein efficient and cost-effective methods for FG detoxification are necessary. Herein, pretreatment methods for reducing FG in crushed whole cottonseed (CWCS) were compared, with residual FG quantified using a sensitive Ultra High-Performance Liquid Chromatography method for detection at trace levels in cottonseed materials. Physical treatment by autoclaving resulted in up to 96% detoxification of FG, without reduction in crude protein (CP) content. Chemical treatment with 1% and 2% Ca(OH)2 eliminated FG to as low as 0.04%, although a reduction in CP content was observed. Similarly, native fermentation, whilst reducing FG content by 99.66% after 6 days incubation, also reduced CP content. In combined physical and biological solid-state fermentation (SSF), basidiomycete fungi Ganoderma lucidum CC351, Panus lecomtei CC40, Pleurotus ostreatus CC389, Pleurotus sapidus CC28 and Pycnoporus sanguineus CC400 all degraded FG in autoclaved CWCS to trace levels often lower than obtained by individual treatments. A reduction in total lipids and increase in CP were also observed, improving nutritional quality. The most efficient fungi, P. ostreatus CC389 and P. lecomtei CC40, secreted considerable laccase and manganese peroxidase enzymes during SSF, potentially involved in FG detoxification. Cost effective, non-polluting, value-adding approaches for FG detoxification offer potential in animal feed industries.