Hydrofluoric and phosphoric acid streams produced by the microelectronic industry usually present high flow and high contents of phosphorus, nitrogen, fluorine, and organic carbon. This study aims at evaluating the efficiency and suitability of alternative process schemes for the treatment and valorization of hydrofluoric and phosphoric acid streams. A comparative approach is proposed, based on the simulation of different process schemes, each involving several steps of physicochemical and biological treatments. The main objectives are to compare (i) the treatment efficiency, (ii) the consumption of chemical reagents, and (iii) the recovery of high-value by-products (e.g. calcium fluoride, struvite, and hydroxyapatite), and hence to identify the most suitable process scheme. Furthermore, this study contributes to the development of chemical precipitation and bioconversion models that can be applied for further simulation studies on wastewater treatment processes. The results indicate that the use of calcium hydroxide (Ca(OH2)) as the only source of Ca2+ and OH− ions for the precipitation steps is a promising way to reduce the total consumption of chemical reagents while recovering high purity (> 98%) calcium fluoride and struvite. Moreover, the use of a membrane aerated biofilm reactor after the precipitation steps may further decrease organic carbon and nitrogen contents below 125 g COD.m−3 and 30 g N.m−3, thus allowing effluent discharge to natural waters. Overall, this study gives useful information for the development of innovative treatment processes, and it provides crucial data for the selection of the most promising alternative schemes.