Amidst the disruptions caused by COVID-19, maintaining learner engagement in traditional and online courses has become a significant concern. This study explores the use of embedded video questions in an undergraduate Biology course grounded in the Learning Experience Design (LXD) pedagogical paradigm with the objective to reduce cognitive load and facilitate cognitive processing in order to promote active learning and knowledge acquisition. Results show that embedded video questions significantly improved quiz grades, participation, and online engagement while reducing mind-wandering and cognitive load. Results also revealed learners' engagement is dependent on their levels of mind-wandering and cognitive load. The study highlights the effectiveness of LX-designed online courses with embedded video questions, emphasizing intentional design decisions for enhancing student learning experiences.