Game-based learning (GBL) has increasingly been used to promote students' learning engagement. Although prior GBL studies have highlighted the significance of learning engagement as a mediator of students' meaningful learning, the existing accounts failed to capture specific evidence of how exactly students' in-game actions in GBL enhance learning engagement. Hence, this mixed-method study was designed to examine whether middle school students' in-game actions are likely to promote certain types of learning engagement (i.e., content and cognitive engagement). This study used and examined the game "E-Rebuild," a single-player three-dimensional architecture game that requires learners' application of math knowledge. Using in-depth gameplay behavior analysis, this study sampled a total of 92 screen-recorded and video-captured gameplay sessions attended by 25 middle school students. We adopted two analytic approaches: sequential analysis and thematic analysis. Whereas sequential analysis explored which in-game actions by students were likely to promote each type of learning engagement, the thematic analysis depicted how certain gameplay contexts contributed to students' enhanced learning engagement. The study found that refugee allocation and material trading actions promoted students' content engagement, whereas using in-game building tools and learning support boosted their cognitive engagement. This study also found that students' learning engagement was associated with their development of mathematical thinking in a GBL context.