Thirty-five Taiwanese undergraduates from an Applied English Department in Southern Taiwan participated in this research. Classroom action research was conducted with multiple methods including focus group interviews, questionnaires, and the teacher’s observations, together with assessments of students’ academic group work and individual writing tasks through the PBL process. It was found that the learning journey was explicitly transformative and troublesome, while the integrative, bounded and irreversible characteristics of a threshold concept emerged during the research process. The dynamics of peer and teacher-student collaborative work also suggested students’ and the teacher’s epistemological, practical, and ontological development associated with the cognitive, affective, and social aspects of learning. The data from this study were combined with existing research relating to critical thinking and the pedagogical implications of PBL to develop a reflexive framework for future practice.