Technological advancements and market pressures are driving the development of pedagogical course design approaches. By using organizational design research into structuring organizations and work processes to improve effectiveness and efficiency, we focus on two structural constructs from organizational design research: standardization (of coordination including active learning components) and centralization (of decisions making for course implementation). This paper examines the impact of changes to these constructs during the conversion of a course from a traditional (face-to-face) to a blended/flipped modality. Findings show that structuring a course based on standardization and centralization can affect the student outcomes in the course. Specifically, revealing no statistical difference in short-term student performance from the traditional lecture approach to the blended/flipped approach; however, lower variability in performance occurred across sections. In addition, a lagged learning effect derived from an exit exam in students' last semester, revealed a statistical difference with students from the blended/flipped approach achieving higher long-term learning scores. We offer this as an argument for the effectiveness of the standardized active learning components embedded within the new course structure.