This paper explores two project-based educational game design initiatives: Baba is Math and Language Tetris, that exemplify how gamification can be leveraged to create meaningful, theory-driven learning experiences beyond conventional edutainment or gamified apps. Developed by interdisciplinary student teams, these games are rooted in project-based learning (PBL) methodology, emphasizing iterative design, research integration, system dynamics and learner-centered innovation. Both games draw from established puzzle formats (Sokoban in Baba is Math, and Tetris in Language Tetris) to teach foundational content in mathematics and Japanese language. Their design is informed by educational theory, particularly Dewey’s Learning-by-Doing, Csikszentmihalyi’s Flow Theory, and Malone & Lepper’s taxonomy of intrinsic motivation. Rather than layering rewards over static content, the games structure learning as an emergent, interactive process, driven by challenge, curiosity, and player agency. As a methodology, the students applied system thinking and system dynamics to model and refine these systems. The student groups developed Causal Loop Diagrams and Stella simulations to examine motivational and learning loops, player progression, and the impact of difficulty scaling. Visual and narrative feedback systems, including in-game mascots and reinforcement mini-games, scaffold learning while supporting emotional engagement. This paper will explore how a pedagogical approach can be integrated while also adopting aspects from commercial games (such as aesthetics or mechanics) without compromising the core pedagogical integrity of the course itself. We will discuss two projects developed for the Gamification course at the Bachelor of Game Technology and Simulation at University of Inland Norway, and go through the different integration aspects, in case others would want to adopt similar approaches for their courses in the future.