A hotly debated topic is the effectiveness of inquiry-based instructional practice in science classrooms on student achievement and motivation. Numerous studies based on multinational large-scale education data show such student-centered instructional practice positively led to students' motivational beliefs but was negatively associated with science achievement. Current literature, however, drew such a conclusion based on the measures of instructional practice from students' perceptions, not teachers, despite teachers being the subject matter experts and actual implementers of classroom activities. Thus, this study examined the relationships between teacher-perceived instructional practice, science motivational beliefs, and science achievement. Specifically, this study investigated the predictive effects of instructional practices on aggregated student motivational beliefs (i.e., self-concept, utility value, and intrinsic value) and science achievement in the classroom context. Moreover, the study explored the contextual effects of student motivational beliefs on science achievement. We examined 3861 eighth graders' data nested within 168 science classrooms in the Korean portion of the latest Trends in International Mathematics and Science Study using multilevel structural equation modeling. The results showed that the inquiry-based instructional approach did not predict science achievement or motivational beliefs at the classroom level. On the other hand, student self-concept and utility value positively predicted individual achievement, while classroom-level utility value statistically predicted average classroom achievement. In other words, the significant effect of classroom-level utility value on achievement was beyond the effect of individual utility value. The unique contributions of the study lie in advancing the science education literature with a fresh reflection on such relationships by using a less examined data source (i.e., teacher perceptions), focusing on the classroom context (i.e., classroom-level science motivational beliefs and achievement), and situating in an underrepresented country (i.e., Korea) in the literature. The results shed light on the discrepancies in the effectiveness of instructional practice perceived by teachers versus students on desired educational outcomes in a learning context. This study also discusses the practical and methodological implications for instructional and motivational research.