Resilience offers a useful lens for studying how human well-being and the systems on which it depends can absorb and recover from a range of shocks and stressors, including events such as the COVID-19 pandemic. Looking beyond the direct effects of observable shocks and individual or household resilience capacities to the meso-level mechanisms that shape impacts on communities, households, and individuals can both guide our understanding of COVID-19 impacts and help leverage findings from the pandemic context to better understand resilience to other food systems shocks, past, present, and future. We develop a conceptual framework for the multiple paths through which observed, exogenous shocks interact with systemic, endogenous mechanisms to influence the resilience of household well-being and supporting food systems. We illustrate this framework with reference to the COVID-19 pandemic and policy responses as they unfolded in three rural study areas in Malawi, Madagascar, and Kenya. Consistent with this framework, we find multiple pathways through which the pandemic shock affected household food security and resilience. Our findings highlight that in some settings, at some points in the multi-stressor trajectory of a shock, the more serious, direct effects – in this case, severe illness and mortality from SARS-CoV-2 – may impact far fewer people than do the substantive, indirect impacts that arise as behaviors, markets, and policies adjust to the shock. These adjustments are necessarily correlated and elicit varied household coping responses. We illustrate the degree to which, from the point of view of rural food systems and households, COVID-19 is a new shock but its massive, broad-reaching impacts manifest through familiar stressors and uncertainties that frequently burden poor rural populations in much of the lowand middle-income world.