Crystalline scorodite is considered one of the safest materials available for the removal and disposal of arsenic. Its formation by biological means represents a promising solution for the treatment of acidic wastewater containing arsenic. In this study, an analysis of the processes that take place in a bioreactor for the biogenic scorodite crystallization was performed using mathematical modeling. The model was fitted to a set of experimental data, including batch and continuous bioreactors using two different thermoacidophilic archaeal strains, showing a successful model prediction capability (0.85 < R2 < 0.97 with 0.001 < p-values for all variables). A parametric analysis showed that the arsenic precipitation rate constant (kAs(V)) was the parameter with no-statistically significant differences between treatments, being the least sensitive parameter. Our results suggest that the regulation of iron oxidation rate is a key factor in the arsenic precipitation process. Therefore, further experimental studies should be carried out in this field to improve reactor productivities. In addition, the model was implemented to simulate the effect of substrate affinity, cell concentration and iron/arsenic molar ratio on iron oxidation, arsenic precipitation, and crystal size, noting that these parameters are critical in process design due to their strong relationship with operating and recovery costs.