This study presents a design-based research approach involving 5 iterations (semester) of implementing design thinking for engaged learning (DTEL) in an animal science capstone course. DTEL scaffolds design thinking into 10 stages for collaborative project-based learning to foster skills like problem solving and teamwork. Across 5 semesters (spring 2021 to spring 2023), student reflections (n = 276) were analyzed to identify aspects that worked well or were challenging. Network analysis visualized relationships (P < 0.05; Q > 0.4) between codes representing strengths, struggles, and alignment with principles from learning theories. Utilizing the relationships between strengths and theory-based principles to address struggles, resulted in changes to the design of the capstone course each iteration (time that the course was taught). The complexity of maps increased over iterations. Initially, struggles were prominent but decreased as responsive design refinements were made. Alignment of student experiences with principles from learning theories grew substantially from the first iteration to the last (theory-related nodes representing 11.4% vs. 24.4% in each network map, respectively), with learning theories also occupying more central positions in the last map (iteration 5) compared to earlier ones (iterations 1 through 4). These changes suggest student experiences increasingly aligned with principles of cognitive constructivism, social constructivism, constructionism, situated learning, and transformative learning. Design principles derived from the 5-iteration study include: 1) allocating most time to hands-on lab work versus lecture, 2) designating a coordinator faculty, 3) scaffolding for instructors unfamiliar with DTEL, 4) emphasizing consistency in processes over grades, and 5) intentionally developing teamwork skills. The study demonstrates the value of design-based research for iteratively refining and studying learning experiences to foster critical skills for undergraduate students in animal science.