This paper is part of the special issue on Teacher Learning and Practice within Organizational Contexts. Shifting instructional practices in elementary schools to include more equitable, reform-based pedagogies is imperative for supporting students' development as science learners. Teachers need high quality professional development (PD) to learn such practices, but research shows considerable variability in the extent to which teachers implement instructional practices learned during PD. Individual teacher characteristics such as self-efficacy may influence teacher learning during PD, but only account for part of the variability. The organizational conditions of teachers' schools and districts may also play a key role in teachers' implementation of new instructional practices. However, because systematic research in this area in science education is still nascent, it is difficult for districts and PD providers to address organizational barriers to professional learning. To meet this need, we conducted an explanatory mixed-methods study using surveys (N = 54) and interviews (N = 19) of elementary teachers engaged in equity-focused, reform-based science PD, testing the degree to which a conceptually framed set of organizational conditions predicted teacher equity self-efficacy and instructional practice alignment. Out of the 11 organizational conditions, only teacher professional impact and their sense of autonomy in their instructional practice explained variance in the outcomes. Qualitative findings showed these relationships to be iterative and recursive, rather than linear. Our findings underscore the essential role of teacher professionalism and sense of agency over commonly cited organizational conditions such as materials and labs in supporting teachers to implement more equitable science instructional practices during PD.