Background: Group affective states for learning are constantly formed through socio-emotional interactions. However, it remains unclear how the affective states vary during collaboration and how they occur with regulation of learning. Appropriate methods are needed to track both group affective states and these interaction processes. Aims: The present study identifies different socio-emotional interaction episodes during groups' collaborative learning and examines how group affective states fluctuate with regulation of learning during these episodes. Sample: The participants were 54 secondary school students working in groups across four science learning sessions. Methods: Multichannel process data (video, electrodermal activity [EDA]) were collected in an authentic classroom. Groups' affective states were measured with emotional valence captured from video data, and activation captured as sympathetic arousal from EDA data. Regulation of learning was observed from the videotaped interactions. Results: The study disclosed four clusters of socio-emotional interaction episodes (positive, negative, occasional regulation, frequent regulation), which differed in terms of fluctuation of affective states and activated regulation of learning. These clustered episodes confirm how affective states are constantly reset by socio-emotional interactions and regulation of learning. The results also show that states requiring regulation do not automatically lead to its activation. Conclusions: By advancing existing understanding of how group level socio-emotional processes contribute to regulation of learning, the study has implications for educational design and psychological practice. Methodologically, it contributes to collaborative learning research by employing multiple data channels (including biophysiological measures) to explore the various dimensions of socio-emotional processes in groups.