Evolution is a cornerstone theory in biology, yet many undergraduate students have difficulty understanding it. One reason for this is that evolution is often taught in a macro-scale context without explicit links to micro-scale processes. To address this, we developed a series of integrative evolution cases that present the evolution of various traits from their origin in genetic mutation, to the synthesis of modified proteins, to how these proteins produce novel phenotypes, to the related macro-scale impacts that the novel phenotypes have on populations in ecological communities. We postulated that students would develop a fuller understanding of evolution when learning biology in a context where these integrative evolution cases are used. We used a previously developed assessment tool, the ATEEK (Assessment Tool for Evaluating Evolution Knowledge), within a pre-course/post-course assessment framework. Students who learned biology in courses using the integrative cases performed significantly better on the evolution assessment than did students in courses that did not use the cases. We also found that student understanding of evolution increased with increased exposure to the integrative evolution cases. These findings support the general hypothesis that students acquire a more complete understanding of evolution when they learn about its genetic and molecular mechanisms along with macro-scale explanations.