Selective removal of multiple counter-ions in a single mixture is highly desirable for many industrial applications but also very challenging. This study focuses on designing monovalent selective anion exchange membranes (AEMs) for the simultaneous separation of F− and Cl− from SO42− using electrodialysis (ED). A series of brominated poly(2,6-dimethyl-1,4-phenylene oxide) (BPPO) polymers with adjusted bromination degrees at benzyl and aryl positions were synthesized, and quaternized with different tertiary amines of varying chain lengths to produce optimized AEMs. Differences in bromination degrees and the chain lengths of the tertiary amines alter the microstructure of AEMs, which influences the anion transport through the developed membranes. Selected AEMs were modified via layer-by-layer (LbL) deposition of poly (sodium 4-styrenesulfonate) (PSS) and poly(allylamine hydrochloride) (PAH) polyelectrolytes to enhance their monovalent selectivity. ED tests were carried out with an equimolar ternary mixture. When 5 layers of deposition were applied, the achieved Cl−/ SO42− and F−/ SO42− selectivities were 11.7 ± 0.2 and 8.3 ± 0.3, respectively, showing significant improvement compared to a commercial monovalent selective ASVN membrane. Experimental results confirm that simultaneously optimizing membrane microstructure and surface can be an effective strategy for the separation of similar counter-ions in an ED process.