This paper introduces Development Led Inquiry (DLI) as an approach to improve situations incorporating relationships between third sector organisations (TSOs) and agricultural scientists, universities, and the public-sector agricultural establishment. There is limited scholarly work on the role of TSOs in agricultural research. Current approaches appear premised on TSOs being researched upon, and recipients of research outcomes rather than partners in generation and application of new knowledge. DLI expands the boundaries of research systems and roles of TSOs as supporters within them. DLI builds on partnerships between NGOs, farmers’ organisations, and women’s associations; it integrates researchers and research organisations to develop, manage and report knowledge generation and application. DLI is dynamic and developmental with learning for all participants central to the process. DLI unsettles current power structures within research systems and sees research and knowledge generation as a supporter rather than leader of development. DLI is embedded in an inquiring systems approach and applies six interrelated conceptual systems thinking tools. The approach emerged from, and was applied in, a twelve-year agricultural research project in India, and was subsequently introduced to, and further developed in a research project in Pakistan.