The Covid-19 pandemic has forced all dentistry faculties to quickly shift to the online supplementation or replacement of traditional modules to pursue education. However, there is limited research evaluating the effectiveness of this education modality on student performance in dental anatomy and manipulation module. Accordingly, it was aimed to compare the influence of different education modalities on the performances of the students enrolled in this module. The students were requested to perform 11 practical assignments throughout the fall term. A total of 220 face-to-face-educated (F2F) and 138 screen-to-screen-educated (S2S) students were included. To evaluate the influence of education modality on the performances of the students, cumulative success scores were calculated and compared using an independent t-test. The grades of the first (maxillary central), sixth (maxillary premolar), and eleventh assignments (mandibular first molar) were also analyzed to understand the manipulation-skill progress of each student within the same year. The grades of above-mentioned three assignments were converted into nominal data (excellent, very good, good, acceptable, and fail) based on certain thresholds, and a chi-square test was conducted. The cumulative success scores in F2F group were significantly lower than those in S2S group (P = 0.02). Differences between the first and eleventh tasks in both education modalities were significant (P < 0.05). The S2S-educated students achieved significantly higher achievement points in the sixth and eleventh assignments (P < 0.001). The S2S education can be suggested as an applicable modality for teaching dental anatomy and manipulation module. However, further work is needed to ascertain whether this result is replicable throughout dental anatomy education.