E-learning is an educational method that improves knowledge innovation by sharing relevant images for advanced learning, especially in a pandemic state. Furthermore, cone-beam computed tomography (CBCT) is a method that gathers medical or dental diagnostic images. This study aimed to analyze the effectiveness of dental anatomy education through a CBCT technology tool, through teachers' and students' perspectives, adjusted according to the disruptions caused by the COVID-19 pandemic. A cohort study and longitudinal exploratory analysis were performed. Forty undergraduate first-year dental students, from the University of Coimbra in Portugal, were selected as per the inclusion and exclusion criteria. Two different teaching methods were applied during an identical time-period: face-to-face lectures complemented by physical models (T1 cohort) and webinar lectures complemented by CBCT images (T2 cohort). Learning outcomes were then studied according to theoretical and spatial orientation contexts. A self-reported survey that focused on students' satisfaction, stress, and support was studied. Both teaching methods were analyzed with paired sample student's t-test and Pearson Correlation Confidence intervals 95% with P < 0.05. Furthermore, exploratory factor analysis (EFA) was used for self-reported satisfaction survey validity and reliability analysis. The learning outcomes between T1 and T2 cohorts were statistically significant, (P < 0.001) corresponding to differences with a large effect degree (r > 0.60). Students' satisfaction, as measured on a six-point Likert scale, was positively influenced by the webinar lectures supplemented with CBCT images (T2 cohort) in a learning context (4.95 ± 0.5) and future applications (5.92 ± 0.27). In conclusion, the webinar approach with CBCT images was more effective and better learning method for teaching dental anatomy.