This study investigated student engagement of STEM-specialized higher education institutions in comparison with students from humanities & social science and STEM majors, respectively. By doing so, the study aimed to find the effects of the characteristics of STEM disciplines and organizational culture of STEM-specialized small-sized institutions on student engagement. The students majoring STEM disciplines, regardless of the organizational types, showed lower reflective-integrative learning experiences compared to students on humanities & social science disciplines. In contrast, students of STEM-specialized institutions reported significantly higher levels of peer relationship and student-faculty interaction in comparison with humanities & social science students and STEM students of general higher education institutions. Finally, the study suggests policy implications for STEM education.