Objective: In this study, we investigated the implementation of project-based learning (PBL) activities in four secondary science, technology, engineering, and mathematics (STEM) education settings to examine the impact of inquiry based instructional practices on student learning. Method: Direct classroom observations were conducted during the 2013-2014 school year in STEM Traditional Courses, a STEM Platform School, an Engineering Optional Program (EOP), and a Virtual STEM Academy (VSA) to measure teacher instructional practices (School Observation Measure) and student engagement (The Rubric for Student-Centered Activities). Results: The four approaches to STEM education showed significant differences in their implementation of PBL, with the EOP and VSA having higher incidences of PBL activities. Additionally, higher-level questioning strategies, higher-order instructional feedback, and integration of STEM subject areas was absent or rarely observed. Conclusions: Components of PBL are missing in STEM education, in traditional and non-traditional STEM courses. In-service teachers may benefit from professional development that enhances their understanding of PBL activities to maximize student learning opportunities.