Virtual Reality (VR) and Augmented Reality (AR) are giving students a whole new way to explore anatomy, making it easier to explore, interact, and understand complex spatial structures. While these tools have great potential, their impact on different levels of user engagement remains unclear. This study examines how VR (IVAL) and AR (AR Anatomy) influence learning experiences by measuring engagement at three stages: basic engagement refers to how interested and usable the tools were, engrossment refers to how emotionally invested and focused they became, and total immersion refers to being fully present and absorbed, with insights gathered from the Immersive User Experience Questionnaire. We conducted a comparative study with 60 medical students to see how their experience levels shaped their interactions with these technologies. The findings show that VR delivers a deeper sense of immersion but has a steeper learning curve, while AR is more accessible for beginners but doesn’t provide the same level of engagement. We found a strong connection between a user’s skill level and how well each technology works for them. More experienced users benefit from VR’s immersive depth, whereas AR offers an easier entry point for those new to interactive learning. This research sheds light on how these immersive tools can support different learning styles and skill levels. It provides practical insights for educators choosing the right technology to enhance anatomy education and improve student engagement.