This case study investigates the impact of Minecraft Education Edition (MEE) on middle school students’ motivation and learning strategies in science, technology, engineering, and math (STEM) subjects through a quasi-experimental mixed-method approach, combining qualitative and quantitative data analysis. The intervention was structured across two complementary settings: a voluntary after-school program and an integrated curricular activity. The after-school program involved two age groups (19 students aged 11–14), each participating in five sessions. The curricular integration occurred in third-grade science classes, with one small group of 7 students. Activities used predefined Minecraft worlds focused on biodiversity, space exploration, cybersecurity, and structural design. Data from the Motivated Strategies for Learning Questionnaire (MSLQ) and qualitative observations revealed a complex pattern of effects. While students showed high engagement, quantitative data revealed a significant decrease in metacognitive self-regulation and an increase in performance anxiety across both groups. The structured curricular setting, however, was associated with gains in cognitive strategies like elaboration. These results suggest that while MEE is a powerful tool for engagement, its effective implementation requires thoughtful pedagogical scaffolding to help students manage its cognitive and social challenges. Further investigation is warranted to optimize its integration into curricula.