Online-only course design has to balance students' needs to experience (1) competence and (2) autonomy as it may affect their motivation. Lecture units can provide structured guidance by being made accessible in a fixed order, or support students' autonomy by providing free access to all lecture units. Online-only courses with lecture units including videos and quizzes can help provide psychology education to diverse populations. This includes nontraditional students who might struggle to attend traditional courses. We used a questionnaire with two vignettes in Study 1 (N = 152) and found that most students preferred free access to lecture units. Yet, using Moodle log data in Study 2 (N = 424) showed that most students did follow structured guidance in an asynchronous online-only course. Combining the assessment of preferences and behavior in Study 3 (N = 159), we replicated the divergence of preferences and behavior. Students preferring structured guidance and students following it in asynchronous online-only courses reported higher intrinsic motivation than students with diverging preferences and study behavior. This suggests that for many students, support through structured guidance does not compromise perceived autonomy. Structured guidance can be useful for course designers to balance students' needs for autonomy and competence.