Background: In many educational settings, professional development (PD) for in-service teachers assumes particular significance in the wake of curricula reform. This is so that teachers are enabled to become familiar with new competencies that are aligned with new learning standards, and also that teachers may be supported in actively reflecting on their practice. In recent years, some models of PD that incorporate the qualities of sustainability, collaboration and classroom-based research have gained popularity. Classroom-based research with teachers, however, is not always considered by teachers themselves to be an attractive or meaningful model for professional development. This is due to the notion that teachers may be hesitant to engage in research, because of reasons that include a lack of time, weak motivation, a sense that it is a low priority and the belief that research results are irrelevant to the immediate needs of the teaching and learning situation. Purpose: This study aimed to challenge this perception by supporting teachers to become empowered to participate in classroom-based research. It was conducted in the context of exploring what needs to be improved in response to recent curriculum reforms in the Philippines. The study set out to analyse the reflections of in-service teachers who considered the significance of their partnership with university science researchers in a year-long, research-based collaborative professional development activity. As the professional development activity was in its early stage of implementation, it was hoped that insights could be gained into the important factors of the activity, to support its development and design. Methods: In this qualitative study, teachers' reflections about their collaborative research-based PD with university researchers were categorised. Data were obtained from audio and video-taped transcripts, supplemented by formal interviews. Qualitative thematic analysis of conversations was strengthened by using the constant comparison method of Grounded Theory in order to formulate themes from the data transcripts. Findings: Results suggested that through collaboration, sustainability, trust and commitment, the teachers recognised the advantages of classroom-based research in the improvement of their instructional capacities. Through the analysis of the teacher reflections, the study yielded three major themes that are significant in the consideration of classroom-based research: (1) increased understanding of classroom dynamics; (2) shared ownership and involvement; and (3) reflective practice to connect and resolve ideas against prior beliefs. With the full involvement of the teachers, it appeared that the classroom research-based PD employed in this study helped to empower teachers and assisted in eliminating negative notions of research: the PD became, instead, an opportunity for immediate learning.