The purpose of the study is to reveal instructors’ design strategies regarding dialogue and structure in asynchronous online courses, uncover how those designs were received by students, and the predictive effects of course design and student motivation on student learning. A sample of 287 college students and two online course instructors participated in the study. The findings showed that course formality and flexibility indirectly predicted student perceived learning outcomes through the roles of subject specific task values, subject specific emotional cost, online learning self-efficacy, and online learning task values. Dialogue with instructors and classmates did not significantly predict student perceived learning outcomes. Results of student and instructor interviews supported the quantitative results and revealed that formality and flexibility of asynchronous online courses were highly appreciated by students, whereas the dialogic practices instructors used received mixed feedback. These findings suggest that course design is critical in asynchronous online learning, and it has positive impact on students’ motivation, emotional well-being, and student learning outcomes. Practical implications for designing asynchronous online courses are discussed in the paper.