In contemporary educational research, literature highlights the effectiveness of augmented reality (AR) technologies in enhancing learning outcomes. The present study aims to investigate the effectiveness of inquiry-based teaching approaches within mixed reality environments. It specifically examines the simultaneous and successive interactive pathway between the real and virtual environments in the teaching of natural science concepts—particularly phenomena related to the Earth’s rotation and orbit. The entire research initiative was based on a self-constructed physical model representing the Earth’s rotation and orbit, designed and built with student participation, as well as a virtual environment developed by the research team. A total of 65 high school students took part in the final study. They used structured worksheets in both physical and digital formats and engaged in cooperative activities that combined guided and open-ended inquiry. Through these activities, they explored and investigated the phenomena of day/night alternation and the changing of seasons. The findings underscore the educational value of both real and virtual environments, while also revealing important differences. Notably, the results emphasize the effectiveness of the mixed reality learning experience, where real and virtual elements interact simultaneously and bidirectionally through a specialized tool. This interaction fosters a balanced coexistence of virtuality and reality, stimulating students’ innate curiosity, enhancing motivation to learn, and leading to improved learning outcomes.