Agricultural science and technology (S&T) is under great scrutiny. Reorientation towards more holistic approaches, including agroecology, has recently been backed by a global international assessment of agriculture S&T for development (IAASTD). Understanding the past and current trends of agricultural S&T is crucial if such recommendations are to be implemented. This paper shows how the concepts of technological paradigms and trajectories can help analyse the agricultural S&T landscape and dynamics. Genetic engineering and agroecology can be usefully analysed as two different technological paradigms, even though they have not been equally successful in influencing agricultural research. We used a Systems of Innovation (SI) approach to identify the determinants of innovation (the factors that influence research choices) within agricultural research systems. The influence of each determinant is systematically described (e.g. funding priorities, scientists’ cognitive and cultural routines etc.). As a result of their interactions, these determinants construct a technological regime and a lock-in situation that hinders the development of agroecological engineering. Issues linked to breaking out of this lock-in situation are finally discussed.