Research shows that when students use core concepts to guide their reasoning, they are able to construct more accurate, mechanistic explanations. However, there is scant research exploring student's perceptions of the usefulness of core concepts. Knowing students' perceptions could be influential in encouraging faculty to adopt core concept teaching strategies. In this study, we investigated how students perceive the usefulness of using the physiology core concepts to guide their reasoning. We collected the perceptions of undergraduate science majors who had completed Introductory Biology II, which was taught using a subset of physiology core concepts. Eleven student volunteers were interviewed using a semistructured protocol, and 22 students provided end-of-semester reflections. Using a constant comparative method, we identified four emergent themes in students' perceptions: core concepts guide reasoning, core concepts support reasoning and learning across topics and disciplines, core concepts build self-efficacy in reasoning, and drawn core concept tools visualize reasoning. These findings suggest that core concepts, when used as tools to reason with, help students explain rather than memorize physiological phenomena, thus supporting deeper learning and transfer of knowledge to novel contexts. We also found that drawn scaffolding tools play a critical role in helping students organize their thinking, making abstract systems more approachable and supporting mechanistic reasoning. This study is the first qualitative analysis examining students' perceptions of the role core concepts of physiology play in their learning and reasoning processes.