Integrated Science, Technology, Engineering and Mathematics (iSTEM) education is a promising approach to attracting more qualified and better motivated students to STEM fields. In this study, we respond to one of the salient challenges facing integrated STEM educational research, namely investigating its educational impact. We developed a large-scale intervention where all STEM components are integrated and examined the impact this integrated STEM curriculum has had on cognitive performances regarding physics, mathematics, technological concepts, and integrated physics and mathematics. In total, 859 grade 9 students, distributed across 39 Flemish different schools, participated in a long-term study. The results of multilevel analyses show that iSTEM education had positive effects on cognitive performance in terms of mathematics knowledge and application and technological concepts. Also, differential intervention effects were found with regard to student characteristics. Since the impact was only apparent after two years, we stress the importance of a long-term integrated STEM approach.