Farmer Producer Companies (FPCs) are new-generation food systems meant to address development concerns in rural India. While FPCs were established on cooperative ideals, legacy power relations often persist, with certain actors exerting decisive control over market connections and resources. As FPCs emerge from their pre-existing socio-economic conditions, their resilience is predicated on maintaining robust value chain relationships. In this study, we applied a multi-layered approach with network tools on field data to investigate the Matthew effect, where cumulative advantages to elites maintain or amplify inequality. We focused on network power discrepancies and democratic participation in two selected natural farming FPCs. Social network analysis (SNA) and two other visualization approaches, Self-organizing Maps and Parallel Categories Plots, have been deployed to analyse the member networks and FPC ecosystems, before and during the CoVID-19 pandemic. The FPC exhibiting a strong Matthew effect, with a legacy of preferential relationships, showed lower resilience under uncertainty compared to the other FPC, whose legacy of grassroots efforts involving marginal and women farmers managed to avert the Matthew effect. The findings offer valuable insights for the local governance of inclusive food systems and have global relevance, especially for addressing SDGs 5 (gender equality) and 10 (reduced inequalities).