Mixed methods research has become increasingly popular in health systems. Qualitative approaches are often used to explain quantitative results and help to develop interventions or survey instruments. Mixed methods research is especially important in low- and middle-income country (LMIC) settings, where understanding social, economic and cultural contexts are essential to assess health systems performance. To provide researchers and programme managers with a guide to mixed methods research in health systems, we review the best resources with a focus on LMICs. We selected 10 best resources (eight peer-reviewed articles and two textbooks) based on their importance and frequency of use (number of citations), comprehensiveness of content, usefulness to readers and relevance to health systems research in resource-limited contexts. We start with an overview on mixed methods research and discuss resources that are useful for a better understanding of the design and conduct of mixed methods research. To illustrate its practical applications, we provide examples from various countries (China, Vietnam, Kenya, Tanzania, Zambia and India) across different health topics (tuberculosis, malaria, HIV testing and healthcare costs). We conclude with some toolkits which suggest what to do when mixed methods findings conflict and provide guidelines for evaluating the quality of mixed methods research.