This contribution takes a critical look at the theory of governance, autonomy and quality management by drawing our attention to the problems and challenges of the system of higher education for agriculture in India. For the Indian policymaking community, which includes the mainstream sections of educational researchers, scientists and educationists and farmers movements, till this day the Indian system of higher education, research and extension for agriculture represents an outstanding example. In theory achieving quality as excellence, as fitness with purpose and as transformation provides a set of rationales for the planning and implementation of educational innovations, mechanisms for funding, arrangements for governance and autonomy to the policymaking community. In higher education, a closer integration of the three missions namely teaching, research and outreach is recommended the way forward for the shaping of arrangements of governance and autonomy. The rationale underlying this understanding of the policymaking community is that the system of higher education could successfully increase production and productivity during the green revolution phase of agricultural development by closely integrating the three missions namely teaching, research and extension in India. The paradox is that educational innovations capable of allowing the rural communities to reduce environmental impact and loss of production, make necessary productivity gains and transform the system of labour, nature and knowledge in directions that are just are not emerging from the same arrangements of governance and autonomy. The author discusses the directions in which the quality management discourse should move in the light of the evidence already available from not only agricultural education but professional education as such.