This article describes a novel method to dealuminate and realuminate H-beta zeolites as catalysts for removing organic acids from bio-oils via their esterification reactions with alcohols. Modified H-beta zeolites were prepared by leaching with solutions of oxalic acid, DL-malic acid, and DL-tartaric acid that have different numbers of hydroxyl groups. The results showed that, while all three organic acids can dealuminate the parent H-beta zeolite, with Al(VI) a atoms and Al(IV) c ones being preferentially removed, they show quite different realumination abilities, with tartaric acid with two hydroxyl groups having the highest realumination ability. The concomitance of dealumination and realumination and their dependence on the hydroxyl group numbers of the organic acids provide the possibility of finely tuning the Al and acidity distributions of the resulting zeolites. Among the three acid treated H-beta zeolites, the one obtained from malic acid leaching exhibited the best performance in catalyzing the esterification reaction between acetic acid and sec-butyl alcohol, attributed to its suitable quantity and density of medium and strong Brönsted acid sites and enhanced aluminum gradient. The catalytic results obtained in a fixed-bed microreactor revealed that the malic acid leached H-beta exhibited dramatically enhanced catalytic performance compared to the commercial ion-exchange resin Amberlyst® 15, demonstrating great potential for industrial application.