<p>Self-learning environments with instructional videos are well-established for procedural skill remediation, but their effectiveness for conceptual understanding of complex concepts has been less examined. This study examines the impact of more or less structured prompts in instructional videos on students’ understanding of variables as generalizers while controlling for effects of students’ individual engagement. A randomized controlled trial with <i>N</i> = 239 students (grades 9–11) compared three self-learning environments covering the same algebraic content—understanding variables and algebraic expressions: a control group with written explanations and practice tasks, a video group with moderately structured prompts, and a video group with highly structured prompts. All groups significantly improved their understanding; however, when accounting for students’ individual engagement operationalized through prompt use, both video groups achieved significantly higher effects than the control group. No significant differences emerged between the two video groups. For students with low pretest scores, the control group proved less inclusive. The findings highlight the potential of video-supported self-learning for conceptual understanding, but also indicate that further design improvements are needed to engage <i>all</i> students.</p>