Drying the biomass produced is one of the critical steps to avoid cell degradation; however, its high energy cost is a significant technological barrier to improving this type of bioprocess’s technical and economic feasibility. This work explores the impact of the biomass drying method of a strain ofPotamosiphonsp. on the extraction efficiency of a phycoerythrin-rich protein extract. To achieve the above, the effect of time (12–24 h), temperature (40–70 °C), and drying method (convection oven and dehydrator) were determined using an I-best design with a response surface. According to the statistical results, the factors that most influence the extraction and purity of phycoerythrin are temperature and moisture removal by dehydration. The latter demonstrates that gentle drying of the biomass allows removing the most significant amount of moisture from the biomass without affecting the concentration or quality of temperature-sensitive proteins.