Teaching-focused professional development (PD) programs offered to undergraduate STEM instructors at higher education institutions aim to improve teaching quality and undergraduate STEM education. Programs of longer duration with scaffolded topics have been noted to be more effective than ad-hoc, single-meeting-single-topic workshops. However, evidence supporting this claim is scarce. This study examines the impact of a long-term, scaffolded PD program on instructors teaching undergraduate STEM courses at a research-intensive university. Through interviews with 22 STEM instructors who completed the innovative PD program at the same research-intensive university, the study addresses the following research question: how did the PD program impact instructors' (1) views on active learning, (2) willingness to implement evidence-based instructional methods (EBIMs), and (3) teaching practices? During the interviews, instructors reported a significant increase in the use of active learning strategies and evidence-based instructional methods (EBIMs) post-PD, feeling more confident, prepared, and supported in implementing these methods, and shifting their focus from content coverage to student-centered learning. Some instructors faced challenges due to time constraints and balancing traditional lecture content, but enhanced teaching practices were evident as instructors refined their teaching approaches to be more intentional, purposeful, and structured, adopting strategies such as backward design and creating specific learning goals. Interviews also revealed improvements in lesson planning, classroom management, assessments, and feedback between instructors and students. Analyzing the study results through the lens of Bandura's Triadic Reciprocal Determinism suggest that long-term, scaffolded PD programs can significantly improve undergraduate STEM education by enhancing instructors' views on active learning, increasing their willingness to use EBIMs, and refining their teaching practices. Thus, this study highlights the need for sustained investment in this type of PD program for undergraduate STEM instructors, contributing to positive transformations in undergraduate STEM education, increases in recruitment, retention, and graduation rates in STEM fields, and the US remain competitive on a global scale.