Algal biorefineries have emerged as a sustainable solution towards addressing the current challenges relating to energy and the environment. Mixotrophic mode of microalgal cultivation can help in the removal of nutrients from wastewater and the capture of CO₂, along with the accumulation of metabolic products such as lipids, starch, and pigments for biofuel and nutraceutical applications. In this study, bioremediation of domestic wastewater was attempted along with the strategic supply of CO₂ for improved microalgal biomass and biodiesel production by Chlorella minutissima. On cultivation of C. minutissima in domestic wastewater, biomass productivity of 255 ± 10.0 mg L⁻¹ d⁻¹ and lipid productivity of 60.4 ± 2.7 mg L⁻¹ d⁻¹ were obtained with 98% COD removal. Subsequently, augmenting wastewater with an optimal dose of mustard deoiled cake hydrolysate (a low-cost nutrient-rich waste) was found to improve the biomass and lipid productivity by 42.9% and 33.1%, respectively, along with 79% COD reduction. Further, strategic feeding of CO₂ at different time intervals was evaluated in order to reduce the lag phase and prolong the log phase in the growth cycle of the microalgae to further enhance the biomass and lipid productivity with more efficient nutrient removal. Among the intermittent CO₂ feeding experiments, Strategy III, where CO₂ (3.5%, v/v) was sparged during the lag phase and also from mid-log phase to harvest, resulted in higher biomass (510 ± 26.0 mg L⁻¹ d⁻¹) and lipid (120.1 ± 2.8 mg L⁻¹ d⁻¹) productivity with 85% COD removal. Thus, this study demonstrates the efficacy of employing a suitable CO₂ feeding strategy along with augmenting with low-cost nutrient-rich waste for improved algal biomass and lipid production with concurrent remediation of domestic wastewater and CO₂.