Propolis (bee glue) is a resinous, sticky, dark-colored material produced by honeybees. Propolis today, due to its medicinal properties, is increasingly popular and is extensively used in food, beverages, and cosmetic products. Besides its numerous positive properties, propolis may also have adverse effects, such as, principally, allergic eczematous contact dermatitis in apiarists and in consumers with an allergic predisposition. In this study, we found appropriate conditions for removing caffeate esters, which are the main allergenic components, from raw propolis. The proposed method consists of the resuspension of propolis in a food grade solvent, followed by a biotransformation based on the cinnamoyl esterase activity of Lactobacillus helveticus. We showed that the reduction of caffeate esters by L. helveticus did not affect the content of flavonoids, which are the main bioactive molecules of propolis. Furthermore, we verified that the biotransformation of propolis did not cause a loss of antimicrobial activity. Finally, we demonstrated that the ability of L. helveticus to hydrolyze caffeate esters in propolis is strain specific. In conclusion, the proposed strategy is simple, employs food grade materials, and is effective in selectively removing allergenic molecules without affecting the bioactive fraction of propolis. This is the first study demonstrating that the allergenic caffeate esters of propolis can be eliminated by means of a bacterial biotransformation procedure.