This study proposes that the gestures of an agent tutor in a multimedia learning environment can generate positive and negative emotions in learners and influence their cognitive processes. To achieve this, we developed and integrated positive and negative agent tutor gestures in a multimedia learning environment directed by cognitive gestures. The effects of emotion type on cognition were examined in terms of cognitive load, learning motivation, and achievement. The subjects were 46 university students in Gyeonggi Province, South Korea. The students were divided into three learner groups: cognition, cognition + negative emotion, and cognition + positive emotion. The learners watched a tutorial lecture on the Notion note-taking app by an agent tutor. Data analysis was conducted using one-way ANOVA to determine the cognitive load, learning motivation, and achievement. The results showed that the positive emotion design was more effective in terms of intrinsic cognitive load, learning motivation, and achievement but had a higher extrinsic cognitive load. However, even the negative + passive group showed more positive learning than the cognition group. Although this study focused on gestures by an agent tutor, it implies that such gestures in multimedia learning contexts must be informed by emotional as well as cognitive design to provide a more meaningful learning experience.