As the global food system causes environmental degradation and contributes to detrimental health effects, transformation is vital for a sustainable and fair future for all. Research on food system transformation and the role of food initiatives has increased. In the food sectors in Stockholm and Cape Town, niche initiatives, commonly also referred to as “seeds” within the “Seeds of Good Anthropocenes” (SoGA) project, are finding new ways to contribute to change in the social-ecological systems in which they operate. The questions addressed in this study are (i) how the transformative capacity of these seed initiatives has evolved over time (ii) what amplifying processes the seed initiatives undertake to increase their impact and (iii) what the enablers and barriers to an effective implementation of those amplifying strategies are. A three-dimensional framework of transformative capacity and a typology of eight amplification processes are used for the analysis. Findings indicate that seed initiatives are building momentum and developing transformative capacity within three areas: ecological processes, social sustainability, and agency and empowerment. The initiatives foremost apply strategies of stabilizing and scaling deep to amplify their transformative impact. Food seeds play an important role in building sustainable food systems and their contribution to change challenges the traditional thinking of growth in transformations and emphasize aspects of changing values, improving quality, and encouraging diversity.