Calls for reform in university education have prompted a movement from teacher- to student-centered course design, and included developments such as peer-teaching, problem- and inquiry-based learning. In the sciences, inquiry-based learning has been widely promoted to increase literacy and skill development, but there has been little comparison to more traditional curricula. In this study, we demonstrated greater improvements in students' science literacy and research skills using inquiry lab instruction. We also found that inquiry students gained self-confidence in scientific abilities, but traditional students' gain was greater--likely indicating that the traditional curriculum promoted over-confidence. Inquiry lab students valued more authentic science exposure but acknowledged that experiencing the complexity and frustrations faced by practicing scientists was challenging, and may explain the widespread reported student resistance to inquiry curricula.