Innovative strategies are needed to improve the delivery of evidence-informed health interventions. Embedded implementation research (EIR) seeks to enhance the generation and use of evidence for programme improvement through four core features: (1) central involvement of programme/policy decision-makers in the research cycle; (2) collaborative research partnerships; (3) positioning research within programme processes and (4) research focused on implementation. This paper examines how these features influence evidence-to-action processes and explores how they are operationalized, their effects and supporting conditions needed. We used a qualitative, comparative case study approach, drawing on document analysis and semi-structured interviews across multiple informant groups, to examine three EIR projects in Bolivia, Colombia and the Dominican Republic. Our findings are presented according to the four core EIR features. The central involvement of decision-makers in EIR was enhanced by decision-maker authority over the programme studied, professional networks and critical reflection. Strong research-practice partnerships were facilitated by commitment, a clear and shared purpose and representation of diverse perspectives. Evidence around positioning research within programme processes was less conclusive; however, as all three cases made significant advances in research use and programme improvement, this feature of EIR may be less critical than others, depending on specific circumstances. Finally, a research focus on implementation demanded proactive engagement by decision-makers in conceptualizing the research and identifying opportunities for direct action by decision-makers. As the EIR approach is a novel approach in these low-resource settings, key supports are needed to build capacity of health sector stakeholders and create an enabling environment through system-level strategies. Key implications for such supports include: promoting EIR and creating incentives for decision-makers to engage in it, establishing structures or mechanisms to facilitate decision-maker involvement, allocating funds for EIR, and developing guidance for EIR practitioners.