BioWin 6.0 does not accurately predict phosphorus (P) speciation in acidogenic anaerobic digesters under default kinetics characterization and parameterization. The accurate modeling of acid-phase digestion is needed to predict the performance of novel nutrient recovery technologies that act on these digester effluents. The main thrust of this work was to identify and correct the causes of inaccurate P partitioning and precipitation within BioWin models of acid-phase digestion reactors. A BioWin configuration including an organic acid digester was parameterized and recalibrated based on the known traits of acid-phase digestion and then validated against a full-scale digester in a municipal wastewater treatment plant. This digester, with pH 5.14 and 61–74% solubilized P, was predicted by BioWin default parameters to have only 27% soluble P and a net formation of P precipitates. Corrections to the polyphosphate-accumulating organism decay, endogenous product decay, hydrolysis rate, and brushite behavior resulted in 67% solubilization with no precipitate formation. Cabinet configurations showed similar behavior when modified to include an acid-phase digester under default parameters, but predictions were similarly amended by our parameter changes. This improved modeling technique should allow operators to effectively characterize acid digesters for their own treatment trains and allow engineers to predict the performance of novel nutrient recovery technologies acting on acidogenic digest.