Research methodology courses can enable students to complete research procedures without necessarily developing the reflective judgment needed to explain, evaluate, and revise methodological decisions. This study examined how the implementation of Transformative Project-Based Learning (TPjBL) shaped students’ reflective competence in a Research Methodology course in English Language Teacher Education. Adopting a qualitative case study design, the study drew primarily on weekly reflective journals produced across the semester, supported by participant observation notes, focus group discussions, students’ project artifacts, and pre- and post-rubric scores as supplementary descriptive data. The data were analyzed thematically to trace recurring patterns and changes in the focus and depth of students’ reflection throughout the TPjBL process. The findings revealed four interconnected developments. Students moved from initial uncertainty toward greater reflective awareness of the relevance and demands of research; they became more deliberate in evaluating the alignment among research problems, questions, literature, methods, instruments, and analysis; their reflections deepened during data interpretation and discussion writing; and peer feedback, revision, and repeated project cycles strengthened ownership and self-monitoring. These findings suggest that TPjBL can function as a reflective pedagogical structure when inquiry, methodological justification, interpretation, feedback, and revision are embedded across the project cycle. The study contributes a process-based account of how reflective competence may develop in research methodology learning rather than treating reflection only as an end-of-course outcome.