Cyanobacterial phosphate accumulation can potentially solve two major problems facing modern agriculture: recovery of valuable phosphorus resources and reduction of ecological damage from nutrient mismanagement. In this work, we present a process for the recovery of phosphorus from dairy manure. Due to the relatively high cost of cyanobacteria cultivation, we explored the impact of several design variables on process performance and determined that increasing phosphate density can serve as an effective solution for reducing process cost. We demonstrated experimentally that by deregulating expression of the phosphate transporter operon pstSCAB we were able to increase phosphate uptake 8.5-fold and maintain phosphate uptake during stationary phase. Even without modifications to polyphosphate production, this strain showed increased accumulation of polyphosphate over wild type during stationary phase. Technoeconomic analysis shows that the new strain reduced process costs by 53%, resulting in a 59% reduction in the levied phosphorus recovery charge. The process also required 68% less energy, 88% less land, and fully eliminated the need for freshwater.