Good teaching practices should not only facilitate learning, but also be effective regardless of students’ family background. This study examines how three dimensions of teaching (instruction, classroom management, and emotional support) interact with students’ socioeconomic status (SES) to predict their science literacy in Indonesian secondary science classrooms. Participants were a nationally representative sample of 6513 students from 236 schools from the PISA 2015 database. Replicating previous studies, multilevel analyses revealed that interactive instruction and classroom management predicted better science literacy, while unguided inquiry-based instruction was associated with lower literacy. Interactive instruction is characterised by student-centered argumentation about science questions, combined with teacher explanations regarding the applications and relevance of science concepts. Meanwhile, unguided inquiry is characterised by student-led investigation activities bereft of teacher guidance. In addition, the current study extends previous literature by showing that interactive instruction is effective in middle and high SES schools, but not in low SES ones. This finding supports social stratification theories which posit that to benefit from student-centered instruction, students need to possess academic dispositions which are rarely socialised in lower SES families. Consequently, policies targeting educational equity should not only concern improvements in instructional quality, but also the preparedness of lower SES students to benefit from instruction.