While there is a global consensus that agricultural systems need to be transformed to be more sustainable, possible pathways and challenges to this process are still debated. We analyse the challenges and opportunities involved in transforming smallholder farming to organic agriculture in Indonesia, where the intense application of Green Revolution technologies came at enormous environmental costs. We adopt a transdisciplinary approach to identify possible pathways towards organic agriculture, based on an analysis of farmers’ knowledge and barriers to adoption, value and belief systems, and institutional structures, including policies and regulations. We present our empirical findings as ‘system knowledge’, ‘target knowledge’ and ‘transformation knowledge’ and incorporate insights from both academics and practitioners. We draw on evidence from large-scale surveys, field experiments, in-depth interviews, participant observation and document analysis. A key insight of our research is that Indonesia does not lack initiatives towards organic farming, but that these various initiatives have different motivations, goals and strategies. This misalignment detracts from the transformational potential of organic agriculture and is responsible for the hitherto limited success of the organic transition. Our findings suggest that policy action at multiple levels is required, guided by an inclusive strategy that is drawn up in a participatory manner.