The promotion of an adequate understanding of science is a central goal of science education, even in elementary school. In this study, we analyzed the effects of a recently developed science intervention program aimed at fostering the understanding of science as well as the motivation of elementary school--aged boys and girls. In prior research, this 10-lesson science course was evaluated with efficacy and effectiveness studies, both of which attested to the positive effects of the program. In this study, we examined the impact of this intervention program after it had been scaled up in educational practice as a continuous element of a STEM enrichment program. In this preregistered trial, we applied a multisite cluster randomized controlled trial with repeated measures to samples of 30 course instructors and 310 third- and fourth-grade students. The children who participated in the intervention program showed better inquiry-related competencies than the children in the waitlist control group while pretreatment scores were controlled for. The intervention program was particularly beneficial for girls such that girls' epistemic beliefs and intrinsic/attainment value in the domain of science tended to improve more than boys'. The results indicated that the intervention program works under real-life conditions and is especially effective for girls.