Project-based learning (PBL) has been suggested as an effective way to engage students meaningfully in science learning. However, there are many challenges when implementing PBL in teaching and learning (e.g., difficulty of assessing learning, students’ hesitation to seek help). This qualitative study investigated how cogenerative dialogues (cogens) can serve as a pedagogical tool to enhance the quality of teaching and learning in a PBL-styled student-scientist partnership program. Data sources included video recording of the internship and cogen activities, field notes, pictures, student journals, and individual interviews. Drawing on cultural-historical activity theory, we identified contradictions tangled with the complex interactions in activities that promoted changes and new developments in teaching and learning. Our analysis of two case studies suggests that cogens help students transform the contradictions in their activity systems into opportunities for becoming active learners, critical thinkers, and collaborative researchers. For transformation to occur, the contradictions must be recognized, reflected, and acted upon. The purposeful discussion about various contradictions in cogens allows participants to deeply reflect on their understandings about learning, teaching, and scientific practice and to disrupt their existing paradigms in order to negotiate new meanings and understandings to support students’ science learning.