Abstract Protein arginine deiminase 4 (PAD4) facilitates the post-translational citrullination of the core histones H3 and H4. While the precise epigenetic function of this modification has not been resolved, it was shown to associate with general chromatin decompaction and to compete with arginine methylation. Recently, we showed that histones are subjected to methylglyoxal (MGO)-induced glycation on nucleophilic side chains, particularly arginines, under metabolic stress conditions. These non-enzymatic adducts change chromatin architecture and the epigenetic landscape by competing with enzymatic modifications. Here we report that PAD4 antagonizes histone MGO-glycation by protecting the reactive sites with oxygen substitution, as well as by converting already-glycated arginine residues into citrulline. Moreover, we show that similar to the deglycase DJ-1, PAD4 is overexpressed and histone citrullination is upregulated in breast cancer tumors, suggesting an additional mechanistic link to PAD4’s oncogenic properties. Significance Metabolic syndromes and diabetes increase the risk for certain diseases such as cancer. However, the mechanism behind this correlation is poorly understood. Methylglyoxal (MGO), a reactive dicarbonyl sugar metabolite found in cells under metabolic stress, can non-enzymatically modify arginine and lysine residues in histone proteins, making it a new epigenetic marker linking metabolism and disease. Histone MGO-glycation induces changes in chromatin architecture and the epigenetic landscape, and abrogates gene transcription. In this study, we found that protein arginine deiminase 4 (PAD4) exhibits dual functions to antagonize histone MGO-glycation: removing glycation adducts from arginines and converting the unmodified side chains into citrulline, which protects them from undergoing glycation. This unprecedented biochemical mechanism demonstrates a potential function of PAD4 in cancer cells.