The molybdenum mining industry discharges a large volume of acidic wastewater containing significant amounts of molybdenum, copper, and other non-valuable metals. In this study, the separation of metal ions (Mo6+, Fe2+, Ca2+, Na+) and recovery of sulfuric acid from molybdenum metallurgical wastewater were investigated via selective electrodialysis (SED) and nanofiltration (NF). A constant voltage of 6 V and volume ratio between the diluent and concentrate chamber of 1:1 was optimized for SED with a highest acid recovery of 89.6% and Mo6+ rejection rate of 98.1%. In contrast, an optimized operating pressure of 1.0 MPa led to highest acid recovery rate of 59.1% and Mo6+ rejection rate of 96.3% in the NF process. The comparison between SED and NF suggests that SED is more competitive than NF for this wastewater treatment with less energy consumption, higher acid recovery rate and higher purity for the recovered acid. Furthermore, coupling NF with SED could reach an acid recovery rate of over 94.2%. Moreover, it was feasible to convert the residual solution of the membrane process into MoO3 nanoparticles by post-treatment. Therefore, it could be concluded that SED and NF are both promising technologies for acid recovery from molybdenum metallurgical wastewater.