In this study, the Spirulina platenesis growth and carbohydrates, proteins, lipids, and chlorophyll production were investigated by using synthetic wastewater via a mixture experimental design using carbon–nitrogen–phosphorus (C:N:P) relation according to the mixing obtained in the experimental space. In addition, a scale-up in the growth of microalgal biomass in a tubular column photobioreactor was carried out. The activation energy was determined by thermogravimetric analysis from the Spirulina platenesis biomass obtained from the experimental design. Also, kinetic growth analysis and thermal hydrolysis of Spirulina platensis biomass were performed for the experimental case where the carbohydrate concentrations were the highest. The stress induced by phosphorus limitation in the synthetic wastewater enhanced intracellular carbohydrates production. It achieves a maximum concentration of 859.59 ± 80.87 mg/L (60.11% w/w) on run 8. The results showed a relation between the activation energy and carbohydrates concentration in biomass. This indicates that the energy required to start the thermal degradation reaction increases as carbohydrate concentration increases. In terms of hydrothermal pretreatment, the temperature increment in the reactor raises the condition to extract carbohydrates from microalgae biomass. In contrast, the temperature increment decreases the reaction rate on the protein extraction. During the hydrothermal pretreatment, the best condition for the carbohydrates extraction in the Spirulina platensis biomass was 140oC for 45 min. At this condition, cell wall hydrolysis needs an energy supply of 18.65 kJ/mol. The development of this process will allow the fractionation of microalgal biomass and extraction of carbohydrates in terms of a biorefinery.