Chlorogenic acid (CQA), the ester of caffeic acid with quinic acid, supplied to human organisms mainly through coffee, tea, fruits, and vegetables, is one of the most studied polyphenols. It is potentially useful in pharmaceuticals, foodstuffs, feed additives, and cosmetics due to its recently discovered biomedical activity. This finding caused new interest in its properties, its isomers, and its natural occurrence. The presented study shows that 5-O-caffeoylquinic acid, during its buffered water extraction, not only undergoes such transformation as isomerization, water molecule addition, and hydrolysis but also reacts with buffer components forming its derivatives. The amount of each formed component depends on the heating time, buffer pH, and buffer type. Although the concentrations of these components are low, they can be mistakenly treated as a new component not previously found in the examined plant or can be a cause of erroneous quantitative estimations of plant composition.