Game-based learning environments (GBLEs) are educational platforms created to promote and scaffold learners’ self-regulated learning (SRL) strategies while learning complex STEM topics. However, learners can still abuse the intended purposes of GBLEs and engage in ‘gaming the system’, deliberate behaviors employed to forgo the learning process while still completing the task at hand. ‘Gaming the system’ is often investigated within intelligent tutoring systems (ITSs), yet these behaviors have been the subject of limited investigation in narrative-based GBLEs. Thus, this study identified two ‘gaming the system’ behaviors from undergraduate students’ (N = 93) gameplay during the narrative-based GBLE, Crystal Island, and examined how their prior knowledge of microbiology and two agency conditions influenced their frequencies of gaming behaviors and their learning outcomes. Results indicated that students with high prior knowledge engaged in significantly more ‘trial-and-error’ gaming behaviors than those with lower prior knowledge. Moreover, we found that students with partial agency engaged in significantly more “trial-and-error’ gaming behaviors than those will full agency; whereas those will full agency engaged in more ‘guessing’ gaming behaviors than those with full agency. These results indicate the importance for identifying contextually driven gaming behaviors, as well as future GBLE scaffolds to adopt real-time, adaptive scaffolding methods based on learner’s active gameplay and SRL (in)efficiency.