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Arctic food systems are increasingly challenged by rapid climate change, loss of food security and subsequent weakening of food sovereignty, and destabilization of Indigenous practices. Despite growing scientific knowledge on Arctic food systems, Indigenous communities continue to struggle with a plethora of sustainability challenges. To develop a systemic understanding of these challenges, we performed a systematic review of 526 articles published between 1998 and 2021 on Arctic Indigenous food systems. We used the leverage points framework to structure our analysis to understand to what extent the existing Western scientific body of literature provides the necessary knowledge to understand the food system characteristics that give rise to the current sustainability challenges. We combined deductive qualitative and inductive quantitative approaches to identify gaps in the systemic understanding of Arctic Indigenous food systems. We characterized existing research across the four levels of systemic depth—parameters, feedbacks, design, intent—and identified promising directions for future research. Our analyses show that research on food systems is clustered within six main domains, we term environmental contaminants, diet and health, food security, food culture and economy, changing socio-ecological systems and marine and coast. Based on our analysis, we identify three directions for future research that we believe to be of particular importance to enable sustainability transformations of Arctic Indigenous food systems: (i) the decolonization of research practices, (ii) acknowledging the significance of systemic interdependencies across shallow and deep leverage points, and (iii) transdisciplinary action-oriented research collaborations directing transformative system interventions.