The food systems and territories of Indigenous Peoples sustain much of the world’s biodiversity, cultivated and wild, through agroecological practices rooted in Indigenous cosmovision and cultural and spiritual values. These food systems have a critical role to play in sustainability transformations but are widely threatened and have received limited research attention. This paper presents the results of four virtual workshops with Indigenous Peoples: a global workshop and local workshops with communities in coastal Kenya, northeast India and southwest China. Indigenous participants highlighted the role of their food systems in resilience to climate change, nutrition, sustainability and resilience to pandemics, and threats from agriculture, development and conservation policies. They called for research on the rapid loss of Indigenous knowledge; Indigenous Peoples’ land rights and food sovereignty; and the impacts of industrial agriculture on Indigenous food systems, stressing the need for decolonial approaches to revitalise Indigenous knowledge. The paper presents a decolonial and interdisciplinary framework for action-research on Indigenous food systems past and present, from farm to plate, drawing on the virtual workshops, Andean decolonising methods and historical approaches. It concludes that decolonising action-research, led by Indigenous Peoples, is urgently needed to reverse the rapid loss of food-related biocultural heritage.