This study, which is part of the special issue on Teacher Learning and Practice in Organizational Contexts, investigated the ways in which urban middle school science teachers' organizational contexts influenced their ability to identify and leverage minoritized students' funds of knowledge (FoK) to facilitate equitable science learning through hybrid discourse. Ten science teachers received professional development from an external, university partner and ongoing professional learning as part of lesson study. We used a multiple case study methodology and applied the Instructional Capacity Framework and the concept of teacher agency to analyze lesson study artifacts (classroom videos, lesson plans, and TeachFX reports) and interviews where teachers described their perspectives on organizational barriers and facilitators to the implementation of hybrid discourse. Findings demonstrate how individual, organizational, and external factors interacted to produce differences in teams' approaches to hybrid discourse and the individual and collective agency they held for engaging in this work. To all teams, teacher agency was needed to challenge organizational culture and schooling norms that historically did not value minoritized students' FoK or opportunities to construct scientific understandings. External policies, especially high-stakes tests, reified this culture, which was, in turn, internalized by teachers and students as actors within the organization. These interacted with teachers' dispositions (e.g., critical reflexivity and perspectives on the value of students' FoK) as well as capacities within their organization generated via lesson study to influence the degree to which teachers exerted agency to implement hybrid discourse. We close by discussing implications for future teacher learning experiences aligned to equitable science instruction.