Invasive species (IS) pose a global threat to biodiversity and human wellbeing. Managing this complex problem at the large scales required—across biomes, jurisdictions and land tenures—is challenging, particularly in developing countries. Innovative approaches that extend management beyond the remit of government are urgently needed. Initiatives which are not currently dominant, which exist at the margins of current mainstream practice, and which offer new ways of thinking and doing, may represent a promising source of inspiration and impact for IS management. Here we identify and analyse these so-called seeds in the context of IS management in South Africa, with the goal of understanding their contribution to IS management and to deeper transformative change. We examine what kinds of bottom-up innovations are currently present, what activities they involve and whom they benefit, what enablers and barriers they face, and in what ways they demonstrate transformative potential. We identified 37 seed initiatives, including technological solutions, alternative uses for IS, stewardship approaches and ways of engaging the public. Seeds are primarily enabled by their social connections, including broad collaborations, investing in networks, and in working with trusted mediators. Key barriers include misaligned or unstable government funding, inappropriate regulatory frameworks, and shortages of skilled personnel. These seed initiatives include many indicators of transformative change, including the ability to restructure systems, be innovative and be highly co-productive. We identify clusters of seeds representing different transformative strengths. This work provides a first insight into how marginal, experimental or bottom-up initiatives could contribute significantly to the impact of IS management in South Africa, and beyond. Supporting the scaling of these initiatives can contribute to transformative change towards more sustainable and just social-ecological futures.