In agriculture, not all sociotechnical niches seek to plant the seeds of further regime transition: Some niches are designed to last as stable subnetworks harboring alternative agri-food systems. However, such niches often interact with sociotechnical regimes, leading to controversies, conflicts, and threats to niches sustainability. This situation calls for proactive governance of niche-regime interactions. We studied the innovation process in the “Corsican clementine” niche, using semi-structured interviews and participant observation. We wondered how local actors have been dealing with three controversial innovations: a clementine variety, a biological pest control method, and a pruning technique. Cross-analysis of the three innovations shows that (i) the niche's innovation pathway can be diverted by regime-driven innovations; (ii) to protect their niche, local actors set collective rules, both formal and informal; and (iii) controversies over technical innovations make niche-regime tensions more visible, leading local actors to make collective decisions for governing the innovation pathway. This study is the first to highlight the key role of sociotechnical controversies in niche governance.