During the COVID-19 pandemic, anatomy educators have demonstrated their ability to respond to face-to-face (F2F) teaching restrictions and offer emergency remote teaching and learning (ERTL) approach. Another educational model that was intensified during COVID-19 was blended learning (BL) which is a combination of F2F and online settings. Studies on the effects of the methods employed during COVID-19 pandemic on anatomy students' learning outcomes are sparse and show slightly similar but nuanced results. There is poor evidence on how the transition to online-only or to BL in response to COVID-19 impacted anatomy students' performance, cognitive load, and embodied learning. The main aim of this longitudinal study is to evaluate the effectiveness of ERTL and BL on anatomy performance in kinesiology students. The second aim of this study was to better understand students' performance in terms of cognitive load embodied learning, and the use of 3D digital tools. The results indicate no significant differences between F2F and ERTL students' performance. However, the results yielded significantly better performance for the BL students in comparison with both F2F (p = 0.001) and ERTL cohort (p = 0.001). The rapid transition to online-only teaching and learning neither enhanced nor deteriorated students' performance. The BL modality appears to be the most efficient. Learning outcomes were discussed in relation to cognitive load, embodied learning, and the use of 3D digital tools.