Plant food residues including trimmings and peels might contain a range of enzymes capable of transforming bio-organic molecules, and thus they may have potential uses in several biocatalytic processes, including green organic synthesis, modification of food physicochemical properties, bioremediation, etc. Although the use of bacterial and fungal enzymes has gained interest in studies pertaining to biocatalytic applications, plant enzymes have been given less attention or even disregarded. In this view, this study aimed at investigating the use of a crude peroxidase (POD) preparation from onion solid by-products for oxidizing chlorogenic acid (CGA), a widespread phenolic acid, various derivatives of which may occur in foods and food wastes. The highest enzyme activity was observed at a pH value of 4, but considerable activity was also observed at pH 2. Favorable temperatures for increased activity varied between 5 and 20 °C. Liquid chromatography–mass spectrometry analysis of a POD-treated CGA solution showed the formation of two major oxidation products, which were tentatively identified as CGA dimers.