The idea that characteristics acquired by an organism during its lifetime can be inherited by offspring and result in evolution is a substantial impediment to student understanding of evolution. In the current study, we performed a preliminary examination of how acquiring physical changes in a question prompt may differentially cue intuitive and scientific justifications of inheritance and evolution and how this varies based on how student learned the concept. Middle school students in a suburban northeastern district (N = 314) either learned about evolutionary change with a category construction task (with different levels of feedback support) or completed a worksheet. Three days later students responded to two free response scenarios (one where a physical change is acquired). Responses were coded based on student justifications for either science accuracy or intuitive nature. Specific reasons were coded by justification type with high inter-rater agreement (k > 0.93). Results showed that students were more likely to apply intuitive reasoning when a physical change was acquired (50%) than if the change was behavioral in nature (16%). Additionally, students who completed the category construction task provided significantly more scientifically accurate justifications about inheritance (M = 1.12) than control students (M = 0.47), and significantly less intuitive justifications (M = 0.67) than control (M = 1.13). Finally, category construction produced the most scientific reasoning when feedback was provided. Taken together, these results suggest that intuitive reasoning is differentially applied based on physical organismal changes, intuitive reasoning is less frequent when learning via category construction, and the category construction task is more effective for this population with the inclusion of feedback.