<p>The alarming rise in atmospheric CO₂ is leading to a dire global climate emergency, resulting in profound disruptions to the ecosystem as well as human health. There is an urgent need to develop and employ a sustainable and greener solution such as microalgae, which has been researched and reported to sequester CO₂ efficiently and produce highly proteinaceous biomass and bioproducts. However, different environmental perturbations and media modifications often affect the growth and metabolism of microalgae, ultimately affecting its biochemical portfolio. This research study mainly focuses on evaluating and enhancing the CO₂ sequestration potential of native microalgae coupled with the accumulation of valuable metabolites without compromising its growth. The current work concentrates on elucidating the effects of nitrate and phosphate dynamics during high CO₂ supplementation on the growth, chlorophyll, α-tocopherol, and fatty acid methyl ester content of indigenously isolated <i>Scenedesmus</i> sp. at different growth phases. The result of this experiment unfolds the impressive CO₂ fixation ability of <i>Scenedesmus</i> sp., and a significant increase of 37.5% in biomass production when exposed to 15% CO₂ supplementation and macronutrient modulation compared to control. Furthermore, the interplay between high CO₂ and nutrient dynamics also stimulated the production of fatty acids such as oleic acid from 1.4% (C₀N_1.5P_0.04) to 64.9% (C₁₅N_1.5P_0.04). The α-tocopherol estimation by HPLC revealed that in high CO₂ conditions, microalgae produced 45.5% more α-tocopherol than control. <i>Scenedesmus</i> sp., an indigenous microalga, could be a potential candidate for an integrated microalgal biorefinery approach, targeting carbon dioxide sequestration, wastewater treatment, and sustainable biofuel production.</p>