Students’ ability to regulate their learning is considered important for the quality of collaborative inquiry learning. However, there is still limited understanding about how students engage in social forms of regulation processes and what roles these regulatory processes may play during collaborative learning. The purpose of this study was to identify when and how co- and shared regulation of metacognitive, emotional and motivational processes emerge and function during collaborative inquiry learning in science. Two groups of three students (aged 12) from a private primary school in Turkey were videotaped during collaborative inquiry activities in a naturalistic classroom setting over a seven-week period, and the transcripts were analysed in order to identify their use of regulation processes. Moreover, this was combined with the analysis of stimulated-recall interviews with the student groups. Results indicated that co- and shared regulation processes were often initiated by particular events and played a crucial role in the success of students’ collaborative inquiry learning. Co-regulation of metacognitive processes had the function of stimulating students to reflect upon and clarify their thinking, as well as facilitating the construction of new scientific understanding. Shared regulation of metacognitive processes helped students to build a shared understanding of the task, clarify and justify their shared perspective, and sustain the ongoing knowledge co-construction. Moreover, the use of shared emotional and motivational regulation was identified as important for sustaining reciprocal interactions and creating a positive socio-emotional atmosphere within the groups. In addition, the findings revealed links between the positive quality of group interactions and the emergence of co- and shared regulation of metacognitive processes. This study highlights the importance of fostering students’ acquisition and use of regulation processes during collaborative inquiry learning.