Since antibiotics show hormesis effects in cyanobacteria at the nanogram per liter concentration level, the possibility for two commonly used antibiotics (sulfamethoxazole and tetracycline) to increase lipid productivity in Synechocystis sp. PCC 6803 was assessed in the present study. The two target antibiotics significantly promoted (p < 0.05) the biofuel productivity of Synechocystis sp. PCC 6803 through the increase of both biomass and lipid content. Sulfamethoxazole and tetracycline significantly stimulated (p < 0.05) cyanobacterial growth by upregulating proteins related to cell differentiation, cell division, and gene expression; significantly enhanced (p < 0.05) the photosynthetic activity by upregulating photosynthesis-related proteins; and significantly increased (p < 0.05) the lipid content in cyanobacterial cells by downregulating carbohydrate catabolic proteins and carbohydrate transport proteins. Due to the altered expression pattern of biosynthesis-related proteins, the two antibiotics increased the proportion of monounsaturated fatty acids, while tetracycline reduced the proportions of saturated and polyunsaturated fatty acids. The changes in fatty acid composition may improve the combustion performance of biofuel. This study provided insights into the application of antibiotics in cyanobacteria-based biofuel production. Graphical abstract.