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This is a methodology paper that describes our approach to conducting design-based research (DBR) with conjecture mapping (Sandoval, 2014). In our work, we leverage iterative conjecture mapping to frame embedded design cycles for two audiences: teachers and students. One design cycle focuses on professional development (PD) to support computational thinking (CT) integration and teacher outcomes. During our PD, we work with teachers to iteratively co-design new CT-integrated science and math units for their secondary classrooms. For both teacher- and student-facing design cycles, we use iterative conjecture mapping, which frames each DBR step: design, implementation, evaluation, and revision of the intervention. We argue conjecture mapping can be used to connect teacher and student outcomes through embedded design cycles.