The current linear economic model is unsustainable, leading to resource depletion and environmental damage. In this context, the bioeconomy offers a circular alternative using biological resources to create a more sustainable system. This study investigates the potential of the fungus Ganoderma resinaceum CS27 in agricultural waste biovalorization for enzyme and prebiotic fiber production. The study evaluated the fungus grown on agave bagasse, orange peel, and nutshell under different fermentation conditions. The results showed promising enzyme production, with laccase activity highest in orange peel under semisolid fermentation (379 U/l). Cellulase and xylanase activities were also detected, demonstrating the fungus’ potential for lignocellulose degradation. Additionally, orange peel showed the highest antioxidant activity (68% 1,1-Diphenyl-2-picrylhydrazine (DPPH) radical inhibition). Additionally, the orange peel medium showed the highest increase in beneficial bacterial populations, suggesting the fungus’ enzymatic activity increased prebiotic fiber content. These findings highlight the potential of using agricultural waste for enzyme and prebiotic fiber production using Ganoderma resinaceum CS27, promoting a more sustainable bioeconomy in Mexico.