Investigation of the nutritional properties, biological activities, volatile compounds and sensory properties of fungal biomass and supernatants obtained from cheese whey powder fermented with Aspergillus oryzae and Neurospora intermedia was aimed in this study. The biomass produced by A. oryzae exhibited higher total lipid (118.54 g/kg) and total essential amino acid (62.05 g/kg) contents improve in comparison to N. intermedia. In contrast, the N. intermedia biomass showed superior bioactive properties, with the highest levels of total phenolics (4.72 mg gallic acid/g dry basis), total flavonoids, (23.85 mg quercetin/dry basis), and antioxidant activities (221.49 mg Trolox/g dry basis). Furthermore, the A. oryzae biomass derived from whey powder significantly enhanced the concentration of 1-octen-3-ol from 15.64 to 129.35 µg/kg, indicating its potential for improving the flavor profiles of food products with a natural mushroom-like aroma. Whey powder fermented with A. oryzae and N. intermedia contained significant amounts of calcium, sodium, and magnesium. The dominant mineral in the supernatant was Mg (7.40–7.90 mg/L) and a distinct fruity aroma was observed especially in the N. intermedia supernatant. These findings highlight the potential of fungal fermentation to convert dairy industry byproducts into nutrient-dense, flavor-enhancing alternatives.