System innovation is a signature feature of agri-food system transformation. Such system innovation often occurs in niches. However, how the “green shoots” of transformation can be detected and appraised through time remains ambiguous. This paper proposes, applies and tests a framework that could be used as a ‘transformation assessment tool’ to evaluate the level of system innovation in a domain of change. The framework is tested against a case study of a Non-Pesticide Management initiative in South India. The framework helps to reveal how, over 20 years, the initiative triggered a number of system innovations that opened a new development pathway, more aligned to environmental sustainability, equity and social inclusion. A critical enabling factor identified for the expansion and “blossoming” of this green shoot was its capacity to flexibly respond and adapt to emergent and largely unknowable agri-food systems dynamics. In its conclusions, the paper sheds light on the ongoing tensions around the defining benchmarks or thresholds for assessing the ‘transformativeness’ of initiatives and change processes. Finding a way of combining qualitative assessments of system changes with quantitative measures of social, economic, and environmental impact could be a valuable vein of research to enhance our understanding of transformative processes and how to enable them.