BACKGROUND: Health system governance is widely recognised as critical to well-performing health systems in low- and middle-income countries. However, in 2008, the Alliance for Health Policy and Systems Research identified governance as a neglected health systems research issue. Given the demands of such research, the Alliance recommended applying qualitative approaches and institutional analysis as well as implementing cross-country research programmes in engagement with policy-makers and managers. This Commentary reports on a 7-year programme of work that addressed these recommendations by establishing, in partnership with health managers, three district-level learning sites that supported real-time learning about the micro-practices of governance - that is, managers' and health workers' everyday practices of decision-making. PAPER FOCUS: The paper's specific focus is methodological and it seeks to prompt wider discussion about the long-term and engaged nature of learning-site work for governance research. It was developed through processes of systematic reflection within and across the learning sites. In the paper, we describe the learning sites and our research approach, and highlight the set of wider activities that spun out of the research partnership, which both supported the research and enabled it to reach wider audiences. We also separately present the views of managers and researchers about the value of this work and reflect carefully on four critiques of the overall approach, drawing on wider co-production literature. CONCLUSIONS: Ultimately, the key lessons we draw from these experiences are that learning sites offer particular opportunities not only to understand the everyday realities of health system governance but also to support emergent system change led by health managers; the wider impacts of this type of research are enabled by working up the system as well as by infusing research findings into teaching and other activities, and this requires supportive organisational environments, some long-term research funding, recognising the professional and personal risks involved, and sustaining activities over time by paying attention to relationships; and working in multiple settings deepens learning for both researchers and managers. We hope the paper stimulates further reflection about research on health system governance and about co-production as a research approach.