The present study aims to improve biomass and biochemical constituents, especially lipid production of Anabaena variabilis and Nostoc muscorum by formulating an optimal growth condition using various concentrations of nutrients (NO3−, PO43− and CO32−) for biodiesel production. The supplementation of the three nutrients by +50% showed the maximum dry weight and biomass productivity, while the macromolecule contents were varied. The depletion of N-NO3− by 50% N-NO3− showed the maximum lipid yield (146.67 mg L−1) in A. variabilis and the maximum carbohydrate contents (285.33 mg L−1) in N. muscorum with an increase of 35% and 30% over control of the synthetic medium, respectively. However, variation in P-PO43− and C-CO32− showed insignificant improving results for all biochemical compositions in both cyanobacteria. A. variabilis was the superior species for lipid and protein accumulation; however, N. muscorum showed the maximum carbohydrate content. Accordingly, A. variabilis was selected for biodiesel production. In A. variabilis, −50% N-NO3− resulted in 35% higher lipid productivity compared to the control. Furthermore, the fatty acid profile and biodiesel quality-related parameters have improved under this condition. This study has revealed the strategies to improve A. variabilis lipid productivity for biodiesel production for small-scale in vitro application in terms of fuel quality under low nitrate levels.