The Maillard reaction (MR) is responsible for the development of color, taste and aroma in bakery products though the formation of numerous aroma compounds such as pyrazines, pyrroles and aldehydes, nonvolatile taste active compounds and melanoidins. In this article, we investigate the effect of quercetin 3β-D-rutinoside (rutin) supplementation, at the level of 5–50 mg per 100 g, of rye-buckwheat biscuits on the formation of phenolics and volatile Maillard reaction products (MRPs) such as pyrazines, furfuryl alcohol and furfural, determined by headspace solid phase microextraction followed by gas chromatography–mass spectrometry (HS-SPME/GC–MS), in addition to the effect on the antioxidant capacity. The study confirmed that rutin was stable under baking conditions as showed by its content in rye-buckwheat biscuits. Supplementation of biscuits with increasing amounts of rutin resulted in the progressive increase of total phenolics and antioxidant capacity measured by DPPH and OxHLIA assays, but it had no effect on their sensory quality. From the eighteen compounds identified by HS-SPME/GC–MS in the volatile fraction of biscuits were quantitated as a compounds-of-interest: methylpyrazine, ethylpyrazine, 2,3-; 2,5- and 2,6-dimethylpyrazines, as well as furfural, furfuryl alcohol and hexanal. The rutin supplementation of biscuits might be one of the factors to influence the formation of both desirable volatile compounds and undesirable toxic compounds. In conclusion, this study indicates for the significant role of polyphenols on the formation of volatile compounds in biscuits with possible future application in the development of healthy bakery products with high antioxidant capacity.