Alperujo, a solid by-product from the two-phase olive oil extraction process, poses significant environmental challenges due to its high organic load, phytotoxicity, and phenolic content. At the same time, it represents a promising feedstock for recovering value-added compounds such as phenols and volatile fatty acids (VFAs). When used as a substrate for white rot fungi (WRF), it also produces ligninolytic enzymes. This study explores the use of two native WRF, Anthracophyllum discolor and Stereum hirsutum, for the biotransformation of alperujo under solid-state fermentation conditions, with and without supplementation of copper and manganese, two cofactors known to enhance fungal enzymatic activity. S. hirsutum stood out for its ability to release high concentrations of phenolic compounds (up to 6001 ± 236 mg gallic acid eq L−1) and VFAs (up to 1627 ± 325 mg L−1) into the aqueous extract, particularly with metal supplementation. In contrast, A. discolor was more effective in degrading phenolic compounds within the solid matrix, achieving a 41% reduction over a 30-day period. However, its ability to accumulate phenolics and VFAs in the extract was limited. Both WRF exhibited increased enzymatic activities (particularly Laccase and Manganese Peroxidase) with the addition of Cu-Mn, highlighting the potential of the aqueous extract as a natural source of biocatalysts. Phytotoxicity assays using Solanum lycopersicum seeds confirmed a partial detoxification of the treated alperujo. However, none of the fungi could entirely eliminate inhibitory effects on their own, suggesting the need for complementary stabilization steps before agricultural reuse. Overall, the results indicate that S. hirsutum, especially when combined with metal supplementation, is better suited for valorizing alperujo through the recovery of bioactive compounds. Meanwhile, A. discolor may be more suitable for detoxifying the solid phase strategies. These findings support the integration of fungal pretreatment into biorefinery schemes that valorize agroindustrial residues while mitigating environmental issues.