Abstract: The goal of this study was to examine 38 undergraduate and graduate students’ note taking and summarizing, and the relationship between emotions, the accuracy of those notes and summaries, and proportional learning gain, during learning with MetaTutor, an ITS that fosters self-regulated learning while learning complex science topics. Results revealed that students expressed both positive (i.e., joy, surprise) and negative (i.e., confusion, frustration, anger, and contempt) emotions during note taking and summarizing, and that these emotions correlated with each other, as well as with proportional learning gain and accuracy of their notes and summaries. Specifically, contempt during note taking was positively correlated with proportional learning gain; note taking accuracy was negatively correlated with proportional learning gain; and confusion during summarizing was positively correlated with summary accuracy. These results reveal the importance of investigating specific self-regulated learning processes, such as taking notes or making summaries, with future research aimed at examining the differences and similarities between different cognitive and metacognitive processes and how they interact with different emotions similarly or differently during learning. Implications of these findings move us toward developing adaptive ITSs that foster self-regulated science learning, with specific scaffolding based on each individual student’s learning needs.