Natural sciences can be difficult to grasp because physical and chemical phenomena can take place across time and length scales that are beyond the reach of human perception. This problem is particularly true for students attempting to learn about microfluidics, a discipline that involves intricate engineering methods and fluid phenomena that are unintuitive and unique to the microscopic scale. New learning paradigms that combine established principles from the learning sciences and mixed reality (MR) technologies may facilitate the understanding of microfluidics and help connect the experimental methods to the underlying physical and chemical processes. Yet only a few studies have implemented learning sciences principles into the design of MR experiences for university laboratory courses. We thus created AL"ETH"A, an interactive and immersive MR learning platform to help students learn about microfluidics and microfabrication techniques. We designed AL"ETH"A to include scaffolding, gamification, control-of-variables, and multimodal representation strategies that are known to enhance intuition building and learning. We hypothesized that MR will enhance student understanding of microfluidics and microfabrication and help them build intuitions about the processes involved at that scale. To test whether AL"ETH"A improved affective learning outcomes, we employed quizzes and surveys and compared the performance of students that participated in the course with MR to that of a cohort using traditional paper protocols. Overall, we measured a greater building of intuition and engagement for MR students. Our new learning platform provides a useful and practical example of how MR can be implemented to learn challenging interdisciplinary topics such as microfluidics.