Significant detrimental effects of agricultural intensification and specialization are becoming increasingly evident. Reliance on monocultures, few varieties, and intensive use of agrochemicals is a major factor in climate change, biodiversity decline, soil health deterioration, and pollution, putting our food system at risk. This requires sustainable agricultural processes, such as crop diversification, to be more rapidly and effectively tested, adopted, and scaled. While these processes are typically introduced at niche level, they often struggle to scale and to induce broader sustainability transitions. In this study, we investigate how scaling may occur, focusing on institutional logics, their changes, and realignment over time. In particular, we applied an abductive research strategy to collect empirical evidence from two in-depth, longitudinal case studies of innovation niches related to crop diversification. Doing so, we show for the first time that, despite their many differences, scaling processes of crop diversification in both niches converge, presenting similar progressions in terms of institutional dimensions, and facing similar obstacles when it comes to value chain formation. While initial experimentation could still be implemented using organizational forms familiar to the lead actors, we discover that a systemic lack of adequate value chain arrangements obstructed the scaling process of crop diversification in both cases. These findings have been used to reflect on the role of value chain relations in scaling processes in sustainability transitions in agriculture.