Protein glycation, oxidative stress and acetyl cholinesterase enzyme (AChE) are closely implicated in the pathogenesis of diabetic complications and Alzheimer's disease. In this study, we synthesized a series of previously unexplored molecular analogues of halogenated quinone and naphthoquinone to investigate their therapeutic potency against protein glycation, free radical production and acetyl cholinesterase enzyme.The study on protein glycation resulted in the identification of two novel antiglycation agents such as 2,3-dichloronaphthalene-1,4-bistriflate (3) and 2,3-dibromonaphthalene-1,4-bis (trifluoromethanesulfonate) (6) with IC50 values less than 16 micromolar range. Moreover, 2,3-dichloro-1,4- naphthoquinone (DCNQ) (1), 2,3-dibromonaphthoquinone (4), 2,3-dibromonaphthalene-1,4-diol (5) and 2,3,5,6-tetrachlorobenzene-1,4-bis(trifluoromethane- sulfonate) (8) exhibited potent antiglycation activity with IC50 values of 54 ± 1.02, 43 ± 0.5, 65 ± 1.00 and 60 ± 1.25 μM, respectively as compared to the standard inhibitor rutin with an IC50 value of 98 ± 1.50 μM. The structure-activity relationship (SAR) demonstrated that the presence of bis-(trifluoromethanesulfonate) as substituents alongwith halogens moieties appreciably influenced inhibitory potential and enhanced the antiglycation potential significantly. On free radical DPPH (2,2-diphenyl-1-picrylhydrazyl) scavenging assay, 2,3,5,6-tetrachlorobenzene-1,4-bis(trifluoromethane- sulfonate) (8), showed significant antioxidant activity with IC50 values 52 ± 1.50 μM. On acetyl cholinesterase inhibition assay, compound 8 and 2,3-dichloronaphthalene-1,4-bistriflate 3, exhibited considerable inhibition with IC50 values of 98 ± 1.00 μM and 124 ± 1.50 μM, respectively. The SAR studies against AChE revealed that the presence of chlorine and trifluoromethanesulfonate both combined together in a compound enhanced its inhibitory activity several folds. In support of experimental observations, molecular docking studies with the active site of acetyl cholinesterase also confirmed the stronger inhibition of compounds 3, and 8 compared to others derivatives. These inhibitors demonstrated hydrogen bonding with Tyr124 and π-π stacking with Tyr341 of the active site residues. In this study, galantamine, rutin and propyll gallate were used as standard inhibitors, respectively.