Research is urgently needed to learn how to improve the emotional climate of science learning by ameliorating excesses of negative emotions, which may lead to students dropping out of school, teachers burning out, and health problems for both groups. This is especially true when teachers and students are situated in highly challenging environments such as project-based learning (PBL) practice. PBL is regarded as an effective way to engage students meaningfully in science learning. However, emotional dissonance between teachers and students can arise because of many challenges in PBL (e.g., difficulty of assessing learning, uncertainty about teacher and student roles). In this study, we investigated how cogenerative dialogues (cogens) served as a pedagogical tool to address emotional issues in a PBL science internship. Data sources included 210 h of video-recorded internship and cogen sessions conducted with one laboratory team. Drawing on "polyvagal theory" and "event-oriented inquiry," this case study shows how educators used cogens as a tool to transform the emotional climate in an internship through respectful communication emphasizing equality, thereby increasing reciprocity, equality, and synchronicity among teachers and students. The findings may help students and teachers regulate their expressions of emotion and enhance the quality of classroom interactions and learning environments.