The human respiratory system involves complex anatomical structures and physiological processes that are difficult to observe directly, creating challenges for students in developing conceptual understanding. This study aimed to describe changes in middle school students’ learning outcomes following instruction supported by Assemblr EDU-based augmented reality on the human respiratory system. A quantitative pre-experimental approach with a one-group pretest–posttest design was employed. Participants were selected through purposive sampling, and learning outcomes were assessed using a multiple-choice achievement test covering remembering, understanding, applying, and analyzing cognitive processes. The data were analyzed descriptively by comparing pretest and posttest performance and evaluating normalized learning gains. The findings showed that students achieved substantially higher learning outcomes after participating in augmented reality-supported instruction, with overall learning gains categorized as high. Improvements were also observed across all cognitive-process categories, although differences among these categories should be interpreted cautiously because of unequal item distribution. These findings indicate that Assemblr EDU can serve as a useful three-dimensional representational resource for supporting the learning of internal anatomical structures when integrated with appropriate explanations and cognitive learning activities. However, because the study did not include a comparison group or inferential analysis, the findings should be interpreted as preliminary evidence of learning changes rather than causal evidence of instructional effectiveness.