In view of the world's immense dependency on non-renewable fossil fuels, the present study explores the prospect of Anabaena variabilis and Microcystis aeruginosa, which represent two distinct groups of cyanobacteria: nitrogen fixers and non fixers, for bioethanol production by analyzing the carbohydrate in their biomass, and maximizing its cellular accumulation inducing nitrate and phosphate stress. Under control condition, reducing sugar constituted 27.6% and 23.4% of the total carbohydrate, followed by glycogen exhibiting contents of 11.6% and 9.7% dry cell weight in the respective species. Cellulose, starch, and hemicellulose were obtained in lower quantities. Although phosphate starvation raised the carbohydrate content to a greater extent, its yield (mg L−1) was severely affected due to the depletion in the biomass. Hence, a biphasic phosphate-starved strategy was implemented generating a maximal carbohydrate content of 63.4% in A. variabilis and 55.1% in M. aeruginosa (compared to 46.2% and 41.4% under control) accompanied by ∼1.3-fold higher yield. Consequently, the bioethanol production in the test cyanobacteria reached 28.2% and 23.9% respectively with ∼1.3-fold higher (volumetric) yield than the control. Analysis of co-products revealed significant production of poly-β-hydroxybutyrate, C-phycocyanin, sodium copper chlorophyllin, and exopolysaccharides, wherein phosphate starvation induced effective stimulation of poly-β-hydroxybutyrate and exopolysaccharides, their yields again enhanced by respective ∼2 and ∼1.4-fold under the biphasic phosphate-starved approach. The present work stands out to be one of its kind comparing the suitability of A. variabilis and M. aeruginosa with an aim to have an overall view on cyanobacteria for bioethanol production by evaluating their carbohydrate profiles under different growth conditions, collectively with the production of various co-products, thus, supporting the bio-refinery concept.