One of the main bottlenecks of a microalgal or cyanobacterial biomass biorefinery is the separation of different useful fractions using simple, low energy-consuming, cost-effective, and scalable separation processes. Although the carbohydrates-rich biomass of these microorganisms presents clear advantages over conventional terrestrial crops as feedstocks for ethanol, it still requires acid and/or enzymatic hydrolysis for efficient fermentation. Here, we show the genetic modification of carbohydrates partitioning in a filamentous cyanobacterium towards the accumulation of sucrose up to 10% (w/w) as a readily fermentable feedstock. We optimized two methods for the preparation of concentrated sucrose syrups, which were efficiently converted into ethanol by yeasts, without the need of additional pretreatments. Biomass drying and milling, followed by aqueous extraction of sugars and proteins, and the recovery of proteins by short pulses of heat, kept the value of sugars as a feedstock for ethanol and protein for feed supplements within a cost-effective biomass biorefinery.