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This study was undertaken to investigate whether chitosan treatments of sprouts of three soybean [Glycine max (L.) Merr.] cultivars (OAC Champion, AC Orford, and AC Proteina) can increase not only concentration of isoflavones in sprouts but also the transcript levels of genes and their subfamilies encoding enzymes at key points of the phenylpropanoid pathway (phenylalanine ammonia-lyase [E.C. 4.3.1.5], chalcone synthase [E.C. 2.3.1.74], chalcone isomerase [E.C. 5.5.1.6], and chalcone reductase [E.C. 2.3.1.170]), and at a key branch-point enzyme in isoflavone biosynthesis (isoflavone synthase [E.C. 1.14.13.86]). Chitosan effects on transcript levels of 14 genes differed depending on the cultivar as demonstrated by significant interactions (P < 0.05) between soybean cultivar and chitosan treatment for all genes. For all cultivars, response to chitosan treatments varied significantly depending on the gene. Overall, the greatest response was observed with high molecular weight chitosan. Very-low- and low-isoflavone cultivars (i.e., AC Orford and OAC Champion) sometimes responded positively to chitosan treatments, while the high-isoflavone cultivar (i.e., AC Proteina) responded only negatively to chitosan. Chitosan treatments had limited effect on isoflavone concentrations, only reducing glycitein in OAC Champion by 38%. No correlation was found between gene expression and isoflavone concentrations. Differences in isoflavone concentrations were observed between sprouts of the three cultivars; AC Proteina had the highest isoflavone concentration and AC Orford the lowest. Results indicate that although isoflavone concentration and gene expression varied with cultivar, chitosan treatment is not a viable option for increasing isoflavone content in sprouts of cultivars evaluated.