BACKGROUND: The Embedded Healthcare Research Conference aimed to promote and enhance research-operations partnerships in diverse health care settings. Within this conference, the Priorities and Methods Workgroup set out to define a vision of embedded research that leverages diverse methods to address clearly articulated research questions of importance to health systems. METHODS: The Workgroup session involved a combination of small and large group discussions around three broadly focused topics: the integration of embedded research within the existing quality improvement (QI) ecosystem; the identification, prioritization and formulation of embedded research questions; the creation of an embedded research "tool kit." RESULTS: Workgroup participants envisioned a future for embedded research that is characterized by authentic engagement between researchers and health system leaders; seamless integration between research, QI and clinical operations; clear and explicit articulation of research questions; an appropriate balance between rigor and relevance in applied methodology; alignment between study design, available resources and the importance of the knowledge to be gained; efficient processes; and bi-directional communication. Important barriers to achieving this vision include limited access to executive leaders, silos that discourage integration of research and QI, generally low tolerance for disruption in high-risk clinical settings, limited access to data, and limited availability of researchers with requisite skills and training. CONCLUSIONS: Embedded research holds potential to enhance the relevance, value and use of research, while also creating generalizable knowledge. Key recommendations include building authentic relationships, discouraging silos, encouraging innovation and experimentation, and expanding opportunities for funding research in delivery systems.