The present study examined how students’ working memory capacity influences learning from animations with or without guidance. We tested three different conditions: visual guidance, instructional guidance, and no guidance. The results show that especially visual guidance was perceived as being helpful for making references between narration and display of an animation. However, students without guidance outperformed both groups of students with guidance on a domain-specific knowledge test. A significant interaction between type of guidance and working memory capacity revealed that visual guidance impeded learning in students with high working memory capacity, whereas instructional guidance impeded learning in students with low working memory capacity. Our results suggest that working memory capacity is an important learner variable that should be taken into account to understand intervention effects and to customize learning environments to learners’ needs.