Interest in inquiry-based science education (IBSE) often pays little heed to the complex power relations that exist within classrooms. A common obstacle to inquiry is that it strongly diverges from current classroom culture and hence, is outside the sphere of teachers' and students' experiences. Teachers and students bring expectations to the classroom that are entrenched in traditional practices and influenced by dynamics of power that exist within all teacher-student relationships. This study, which emerged during a wider study of the use of a Virtual Chemistry Lab in supporting IBSE, explores how classroom discourse constructs and maintains power relations that either stifle or facilitate inquiry-based approaches in two science lessons. Research methods included teacher interviews, student focus groups, video-recorded lessons, and student self-assessments. Findings indicate distinctive features of power inside the classroom that impact on inquiry-based instruction, such as predominant teacher monitoring on task completion over task understanding, lack of student engagement in ownership of scientific ideas, and prevailing norms of what effective teacher questioning is. We discuss implications for IBSE change efforts, highlighting that well-established power relations currently represent an important limiting factor in the capacity of teachers' IBSE implementation.