A plethora of literature exists identifying the importance of engaging students in learning within Science, Technology, Engineering, and Math (STEM) undergraduate courses, making professional development (PD) for faculty teaching these courses vital. Yet few studies of PD programs focus on STEM faculty, incorporate direct measures of faculty practice, and seek to understand the student experience in courses taught by these faculty. In this study, I examine the impact of a program for faculty teaching large enrollment STEM courses on their perceptions, instructional practices, and student perceptions of learning. The program included a week-long course design institute (35 hrs) and a year-long STEM Faculty Learning Community (STEM-FLC) that met monthly (14 hrs). Data included faculty surveys, course syllabi, observations of teaching, and Student Evaluations of Teaching (SETs). Results suggest the program helped instructors create more learning-focused courses and implement student-centered instructional practices to differing degrees. Despite the STEM-FLC, faculty still perceived barriers to implementing their course design. Students' perceptions of course instruction and self-reported learning in these courses highlighted the importance of in-class activities. Finally, when the course design and instructional practice were aligned, students had more positive perceptions and reported higher learning gains compared to students in courses with misalignments in design and practice. Based on the findings of the study and connection with PD literature, I provide a set of essential PD features that may enable STEM faculty to make meaningful and lasting changes to practice.