Project‐Based Learning (PjBL) has been shown to be an effective method to enhance student learning, particularly in science and engineering (S&E) fields. However, the implementation of a PjBL environment plays the deciding role in the students’ interest and learning outcomes. This paper presents a comparative study of two PjBL courses, Physics Laboratory and Engineering Design, which have similar intended goals and features but different implementation related to self‐direction and student autonomy. Classroom observations and interviews with both students and faculty are analyzed using Grounded Theory. Stefanou et al.’s framework of autonomy support within the PjBL paradigm is identified as a data source and is then used to analyze both courses. We further discuss the implications of the course goal implementations on student interest and affect, and argue for a more comprehensive PjBL model in introductory college‐level S&E courses.