The aim of this study was to evaluate the potential industrial applicability of the green microalga Graesiella emersonii GEGS21 by comparing its biomass, photosynthetic pigments, and biodiesel properties under photoautotrophic (PA) and heterotrophic (HT) cultivation. Four agricultural soluble fertilizers (SFs) were tested as substitute medium for algal growth. Of these, three were not only cost-effective but also more efficient in promoting growth compared to the BG-11 algal medium. Supplementing the SF medium with 12 g/L of glucose significantly improved algal biomass productivity under HT condition, and the optimal conditions were identified as 0 M NaCl, a temperature of 30 °C, and a pH of 8. Subsequent supplementation with yeast extract led to a notable enhancement in algal growth, resulting in approximately 18.6-times higher biomass productivity compared to the PA condition. Under HT cultivation, the productivities of the photosynthetic pigments including lutein and zeaxanthin were significantly increased approximately by 3.6-fold and 3.5-fold, respectively compared to the PA condition (p < 0.05). Moreover, HT cultivation led to improved biodiesel properties, such as iodine value, cetane number, oxidative stability, and kinematic viscosity. These enhancements, achieved through altered fatty acid methyl ester composition, align with the ASTM D6751 and EN14214 biodiesel standards. Interestingly, when cultivated under HT conditions, algal strain exhibited higher sedimentation efficiency, accompanied by an enhanced cellular starch content, compared to both PA and mixotrophic conditions. This suggests a promising strategy for economically viable harvesting by altering the specific gravity of algal cells. In conclusion, our findings suggest that HT cultivation of Graesiella emersonii GEGS21 may serve as an effective approach to produce value-added compounds and bioenergy, offering potential for economical harvesting.