Self-regulated learning (SRL), or learners' ability to monitor and change their own cognitive, affective, metacognitive, and motivational processes, encompasses several operations that should be deployed during learning including Searching, Monitoring, Assembling, Rehearsing, and Translating (SMART). Scaffolds are needed within GBLEs to both increase learning outcomes and promote the accurate and efficient use of SRL SMART operations. This study aims to examine how restricted agency (i.e., control over one's actions) can be used to scaffold learners' SMART operations as they learn about microbiology with Crystal Island, a game-based learning environment. Undergraduate students (N = 94) were randomly assigned to one of two conditions: (1) Full Agency, where participants were able to make their own decisions about which actions they could take; and (2) Partial Agency, where participants were required to follow a pre-defined path that dictated the order in which buildings were visited, restricting one's control. As participants played Crystal Island, participants' multimodal data (i.e., log files, eye tracking) were collected to identify instances where participants deployed SMART operations. Results from this study support restricted agency as a successful scaffold of both learning outcomes and SRL SMART operations, where learners who were scaffolded demonstrated more efficient and accurate use of SMART operations. This study provides implications for future scaffolds to better support SRL SMART operations during learning and discussions for future directions for future studies scaffolding SRL during game-based learning.