The incumbent water stress scenario imposes wastewater valorisation to freshwater, promoting technology for its effective treatment. Wastewater from fertiliser factories is quite problematic because of its relevant acidity and solute content. Its treatment through vacuum membrane distillation (VMD) was evaluated through laboratory scale tests at 40 °C and 25 mbar vacuum pressure with polytetrafluoroethylene and polypropylene flat-sheet porous membranes. The wastewater from a partially disused Italian industrial site was considered. VMD distillate fluxes between 22 and 57.4 L m−2 h−1 (LMH), depending on the pore size of the membranes, along with very high retention (R > 99%) for anions (Cl−, NO3−, SO42−, PO43−), NH4+, and chemical oxygen demand (COD) were observed. Laboratory scale reverse osmosis (RO) tests at 25 °C and increasing of the operating pressure (from 20 bar to 40 bar) were carried out with a seawater desalination membrane for comparison purposes. Permeability values around 1.1 LMH/bar almost independently of the operating pressure were observed. Lower retentions than those measured from VMD tests were found. Finally, for any given RO operating pressure, the flux recovery ratio (FRR) calculated from permeate fluxes measured with pure water before and after wastewater treatment was always much lower that evaluated for VMD membranes.