Silver nanoparticles have antimicrobial properties since they can be regarded as an efficient protector against pathogenic microorganisms. Fourier transform infrared spectroscopy was used to examine conformational changes in the secondary structure of wheat gluten washed out from grain treated with an aqueous solution of silver nanoparticles stabilized by trisodium citrate. Silver nanoparticles were used as a protective layer on the grain surface against bacterial and fungal infections (antimicrobial agent). Analysis of the amide I band revealed significant changes in the secondary structure after using silver nanoparticles. An increase in the β-sheet content (from 36.2 to 39.2%) was observed at the expense of the  α-helix and β-turn content. To find factors causing these changes, the wheat grains were treated by an aqueous solution of trisodium citrate and water. The results obtained indicate that the changes in the gluten structure were connected mainly with the trisodium citrate action due to presence of a small number of free molecules of the stabilizer in the solution of silver nanoparticles. Additionally, the conformational changes in gluten pointed out that gluten flexibility increased (decrease in the αH/βS ratio from 1.40 for the control sample to 1.26 for the silver nanoparticle-treated samples) as well as the solubility of gluten decreased (decrease in the β-turn content from 13.1 to 11.4%).