In this study, a simple method for the fabrication of highly diffusive, adsorptive and conductive eco-friendly polyelectrolyte membranes (PEMs) with sulfonate functionalized pectin and poly(vinyl alcohol)(PVA) was established. The graft-copolymers were synthesized by employing the use of potassium persulfate as a free radical initiator from pectin (PC), a carbohydrate polymer with 2-acrylamido-2-methyl-1-propanesulphonic acid (AMPS) and sodium 4-vinylbenzene sulphonate (SVBS). The PEMs were fabricated from the blends of pectin graft-copolymers (PC-g-AMPS and PC-g-SVBS) and PVA by using a solution casting method, followed by chemical crosslinking with glutaraldehyde. The composite PEMs were fabricated by mixing phosphomolybdic acid with the aforementioned blends. The PEMs were successfully characterized by FTIR, XRD, SEM, and EDAX studies. They were assessed for the controlled release of an anti-cancer drug (5-fluorouracil) and the removal of toxic metal ions (Cu2+) from aqueous media. Furthermore, the composite PEMs were evaluated for fuel cell application. The 5-fluorouracil release capacity of the PEMs was found to be 93% and 99.1% at 300 min in a phosphate buffer solution (pH = 7.4). The highest Cu2+ removal was observed at 206.7 and 190.1 mg/g. The phosphomolybdic acid-embedded PEMs showed superior methanol permeability, i.e., 6.83 × 10−5, and 5.94 × 10−5, compared to the pristine PEMs. Furthermore, the same trend was observed for the proton conductivities, i.e., 13.77 × 10−3, and 18.6 × 10−3 S/cm at 30 °C.