The effectiveness of augmented reality (AR) in anatomy and histology education remains variable across literature, suggesting strong dependence on pedagogical context, learner characteristics, and conditions of use. ARanatomy was developed as a mobile AR-learning environment to support spatial understanding of anatomical structures across multiple levels of organization, from macroscopic to histological, and required contextualized evaluation under authentic curricular conditions. This multicentric study involved 2,031 students across five cohorts from three institutions across Europe and Sub-Saharan Africa. Three successive versions of the application were deployed, differing in ergonomic maturity and level of usage instrumentation. Collected data included student perceptions (WBLT framework), motivation (Self-Determination Theory), objective usage traces, and performance outcomes when available. Descriptive, comparative, and correlational analyses were conducted, and usage profiles were identified using K -means clustering ( k = 3). Perceptions of learning and design varied markedly across cohorts. Engagement differences between users and non-users were limited. Instrumented analyses showed that intensive and diversified use was associated with higher visuospatial performance, whereas no effect was observed on immediate disciplinary performance. Usage intensity correlated positively with intrinsic motivation and positive emotions and negatively with amotivation. These findings indicate that the educational value of ARanatomy depends primarily on its pedagogical integration, ergonomic maturity, and depth of use. AR was associated with higher visuospatial performance than with short-term academic performance, although no causal relationship could be established. Taking together, these results highlight the importance of analytics-informed and pedagogically aligned implementation in anatomy education.