Vinasse, a high-strength byproduct of the sugar–ethanol industry, was simultaneously valorized and remediated using the edible filamentous fungus Neurospora intermedia. Optimal cultivation conditions (6°Brix vinasse, pH 7, 0.5 g/L KNO₃, 1% inoculum, and 1 g/L diammonium citrate) produced 14.9 g/L fungal biomass enriched with carotenoids (76.38 μg/g) and vitamins B1, B2, B3, and B6. The process reduced vinasse COD by 63% and enabled substantial minerals bioaccumulation, removing up to ∼65% of Mn and Ca. FTIR analysis confirmed melanoidin adsorption, while SEM revealed thinner, highly branched hyphae under vinasse stress. Post-treatment with activated carbon or Purolite A502PS resin achieved >94% decolorization. This integrated system converts a problematic effluent into nutrient-rich biomass while improving wastewater quality, offering a practical circular-bioeconomy strategy for the sugar–ethanol sector.