This qualitative longitudinal study explored three engineering instructors' professional agency in implementing project-based learning (PBL), including multiple sets of data (18 interviews, observations, and written reflections spanning three semesters). The results show that the instructors' care for students, interest in pedagogical innovation, and efforts in professional learning supported their confidence in stance, sense of agency, and competence in PBL practice. The efficacy and strong beliefs of the instructors further supported their agency-in-action regarding how they acted to influence their teaching by negotiating both its content and conditions. The study also revealed how individual resources and social conditions frame the enactment of professional agency and how the instructors developed agency and strategies to overcome challenging issues at work. Although they developed different types of agency, they demonstrated the same attitude towards resilience and negotiation for autonomy as well as the same engagement in self-empowerment and transforming their agentic competence into educational leadership.