The COVID-19 pandemic has globally jeopardized food security, with heightened threats for the most vulnerable including smallholder farmers as well as rural, indigenous populations. A serial cross-sectional study was conducted to document effect of COVID-19 pandemic on food environment, agricultural practices, diets and food security, along with potential determinants of food systems resilience, among vulnerable smallholder farmer households in indigenous communities of Santhal, Munda, and Sauria Paharia of Jharkhand state, India. Telephonic household surveys were conducted in two phases i.e., lockdown and unlock phase to assess the impact of the pandemic on their food systems and agricultural practices. Market surveys were conducted during the unlock phase, to understand the impact on local informal markets. Secondary data on state and district level food production and Government food security programs were also reviewed. For data analysis purpose, a conceptual framework was developed which delineated possible pathways of impact of COVID-19 pandemic on food environment, food security and food consumption patterns along with factors that may offer resilience. Our findings revealed adverse effects on food production and access among all three communities, due to restrictions in movement of farm labor and supplies, along with disruptions in food supply chains and other food-related logistics and services associated with the pandemic and mitigation measures. The pandemic significantly impacted the livelihoods and incomes among all three indigenous communities during both lockdown and unlock phases, which were attributed to a reduction in sale of agricultural produce, distress selling at lower prices and reduced opportunity for daily wage laboring. A significant proportion of respondents also experienced changes in dietary intake patterns. Key determinants of resilience were identified; these included accessibility to agricultural inputs like indigenous seeds, labor available at household level due to back migration and access to diverse food environments, specifically the wild food environment. There is a need for programs and interventions to conserve and revitalize the bio-cultural resources available within these vulnerable indigenous communities and build resilient food systems that depend on shorter food supply chains and utilize indigenous knowledge systems and associated resources, thereby supporting healthy, equitable and sustainable food systems for all.