The development of new composite membranes is required to separate chemical species from aggressive environments without using corrective reagents. One such case is represented by the high hydrochloric acid mixture (very low pH and pCl) that contains mixed metal ions, or that of copper, cadmium, zinc and lead ions in a binary mixture (Cu–Zn and Cd–Pb) or quaternary mixture. This paper presents the obtaining of a composite membrane chitosan (Chi)–sulfonated poly (ether ether ketone) (sPEEK)–polypropylene hollow fiber (Chi/sPEEK/PPHF) and its use in the separation of binary or quaternary mixtures of copper, cadmium, zinc, and lead ions by nanofiltration and pertraction. The obtained membranes were morphologically and structurally characterized using scanning electron microscopy (SEM), high resolution SEM (HR–SEM), energy dispersive spectroscopy analysis (EDAX), Fourier Transform InfraRed (FTIR) spectroscopy, thermogravimetric analysis, and differential scanning calorimetry (TGA-DSC), but also used in preliminary separation tests. Using the ion solutions in hydrochloric acid 3 mol/L, the separation of copper and zinc or cadmium and lead ions from binary mixtures was performed. The pertraction results were superior to those obtained by nanofiltration, both in terms of extraction efficiency and because at pertraction, the separate cation was simultaneously concentrated by an order of magnitude. The mixture of the four cations was separated by nanofiltration (at 5 bars, using a membrane of a 1 m2 active area) by varying two operational parameters: pH and pCl. Cation retention could reach 95% when adequate values of operational parameters were selected. The paper makes some recommendations for the use of composite membranes, chitosan (Chi)–sulfonated poly (ether ether ketone) (sPEEK)–polypropylene hollow fiber (Chi/sPEEK/PPHF), so as to obtain the maximum possible retention of the target cation.