The interaction of the model flavonoid glycoside rutin with the flavonoid reagent diphenylborinic acid 2-aminoethyl ester (DPBA) was investigated using a combination of HPLC–DAD–ESI–MS analysis, UV–visible spectroscopy, and semiempirical calculations. Mass spectra and spectroscopic data made it possible to describe the complexation pathway as addition of diphenylboron groups to the two available 3′,4′-o-diphenolic and the 5-hydroxy-4-keto coordinating sites of rutin. Semiempirical calculations were carried out to obtain the conformation of the most stable DPBA/rutin adducts. The results showed that a number of complexation dynamics can occur as a function of the characteristics of the medium (type and pH of the solvent) and of the amount of DPBA. This work suggests the possibility of substantially improving existing procedures for recognition of flavonoid compounds by choice of suitable experimental conditions.