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Game-based learning environments (GBLEs) are reported to have high potential for engaging students in meaningful learning. Nevertheless, the investigation of learner emotions during complex learning with GBLEs is much at its infancy. This study examined the change in students’ emotional states during three stages of problem-solving while learning microbiology with a GBLE by using real-time students’ facial behavior data. Results from repeated-measures ANOVA showed significant task effects on learner emotion. We observed the persistency in both negatively-valenced emotions and students’ task behavior across three problem-solving events. This study aims to help us better understand the relationship among learner emotions, task features and task behaviour, and therefore, we can incorporate affect into instructional strategies to promote learning.