Synchronous Distance Learning (SDL) is becoming more and more popular in the academic environment, but comparisons of the effects of this type of learning with those of traditional face-to-face have often been limited to academic performance and satisfaction. The aim of this study is to compare the effects of these two learning modalities on cognitive outcomes (knowledge acquisition, cognitive engagement), affective outcomes (emotions, motivation) and behavioural outcomes (student-teacher interactions, spatial presence). For this, two binary logistic regression models were performed on data from 43 face-to-face and 44 SDL university students (Bordeaux, France) taking courses in cognitive science, neuroscience or ergotherapy. The levels of knowledge acquisition and student-teacher interactions were similar, with tendencies to be respectively superior in face-to-face and SDL modality. In face-to-face conditions, students showed higher levels of cognitive engagement, spatial presence and anxiety. In SDL condition, students showed higher levels of enjoyment, but also higher levels of shame. These results, their practical impact on teaching and directions for future work are discussed.