Recovery of bioactive compounds from microalgal waste represents a sustainable approach for producing value-added nutraceuticals. In this study, natural anti-inflammatory and antioxidant compounds were extracted from the defatted biomass (DB) of ultrasonic-pretreated, municipal-wastewater-grown double mutant Neodesmus pupukensis DMA5 through submerged fermentation (SmF) using immobilized Bacillus stearothermophilus assisted by zinc oxide nanoparticles (ZnO-NPs). The extract was characterized by Fourier-transform infrared (FTIR) and evaluated for its in vitro anti-inflammatory and antioxidant activities, with corresponding IC50 values determined. Maximum total phenolic content of 61.37 ± 0.09 mgGAE/g DW and total flavonoid content of 57.77 ± 0.11 mgQE/g DW were obtained from the DB using immobilized B. stearothermophilus, surpassing those from conventional methanolic extraction. This enhancement correlated with elevated cellulase activity (82.43 ± 0.11 U/mL) observed during SmF. The extract exhibited potent anti-inflammatory and antioxidant activities, with IC50 values of 52.6 µg/mL (albumin denaturation), 57.5 µg/mL (proteinase inhibition), 50.0 µg/mL (lipoxygenase inhibition), 41.6 µg/mL (DPPH), and 46.8 µg/mL (ABTS). FTIR analysis confirmed the presence of hydroxyl, carbonyl, aromatic, and ether functional groups, indicating the enrichment of phenolic, flavonoid, and polysaccharide derivatives responsible for the observed bioactivities. Overall, SmF with immobilized B. stearothermophilus and ZnO-NPs supplementation offers an efficient, eco-friendly, and solvent-free strategy for recovering anti-inflammatory and antioxidant compounds from microalgal DB, highlighting their potential applications in nutraceutical and functional food formulations.