Although there is a large body of research on the effectiveness of supplemental instruction for college undergraduates, very little of it has focused on transfer students, who often confront additional sources of stress and historically perform more poorly than their native student counterparts. In this study, we investigated the effectiveness of a peer-based supplemental instructional program in general and organic chemistry at a large state university over a six-year period, while considering differences across transfer and nontransfer students. The results suggest that the supplemental instruction improved outcomes overall but that nontransfer students benefit to a greater degree than transfer students, in the form of higher grades and pass rates, from attending supplemental instruction. The results suggest that peer-based supplemental instruction is a useful method to improve undergraduate student performance in chemistry, but more research is needed on ways to enhance the effectiveness of interventions in improving the performance of transfer undergraduate students in STEM fields.