Sunflower extraction meal (SEM) is an economically interesting protein source. During alkaline extraction of proteins, the presence of chlorogenic acid (CQA) in the meal gives rise to the formation of o-quinones. Reactions with nucleophiles present in proteins can lead to green discoloration. Although such reactions have been known for a long time, there is a lack of information on the chemical nature of the reaction products. SEM and model systems consisting of amino acids and CQA were subjected to alkaline treatment and, for comparison, to oxidation of CQA by polyphenoloxidase (PPO). Several green trihydroxy benzacridine (TBA) derivatives were tentatively identified in all samples by UHPLC-DAD-MS/MS. Surprisingly, in alkaline-treated samples of particular amino acids as well as in SEM, the same six TBA isomers were detected. In contrast, the enzymatically oxidized samples resulted in only three TBA derivatives. Contrary to previous findings, neither peptide nor amino acid residues were attached to the resultant benzacridine core. The results indicate that the formation of TBA derivatives is caused by the reaction between CQA quinones and free NH2 groups. Further research is necessary to elucidate the structure of the addition products for a comprehensive evaluation of food and feed safety aspects.