As online courses become more common, practitioners are in need of clear guidance on how to translate best educational practices into web-based instruction. Moreover, student engagement is a pressing concern in online courses, which often have high levels of dropout. Our goals in this work were to experimentally study routine instructional design choices and to measure the effects of these choices on students’ subjective experiences (engagement, mind wandering, and interest) in addition to objective learning outcomes. Using randomized controlled trials, we studied the effect of varying instructional activities (namely, assessment and a step-through interactive) on participants’ learning and subjective experiences in a lesson drawn from an online immunology course. Participants were recruited from Amazon Mechanical Turk. Results showed that participants were more likely to drop out when they were in conditions that included assessment. Moreover, assessment with minimal feedback (correct answers only) led to the lowest subjective ratings of any experimental condition. Some of the negative effects of assessment were mitigated by the addition of assessment explanations or a summary interactive. We were surprised to find no difference between the experimental conditions in learning outcomes, but we did find differences between groups in the accuracy of score predictions. Finally, prior knowledge and self-rated confusion were predictors of post-test scores. Using student behavior data from the same online immunology course, we corroborated the importance of assessment explanations. Our results have a clear implication for course developers: the addition of explanations to assessment questions is a simple way to improve online courses.