Crisis mortality events such as disease epidemics and famines have long had major impacts on human health and demography, and clarifying variation in susceptibility to crisis mortality is crucial for enhancing our understanding of the larger-scale phenomena of human adaptation and biological variation. Previous bioarchaeological research using data from human skeletal remains has revealed variable patterns of biological, and by inference, social determinants of vulnerability to medieval famine and plague mortality. However, such previous work did not account for missing data and the potential associated biases. For this study, we apply a novel approach integrating dietary isotope, pathological, and demographic data into multinomial logistic regression analyses of mortality differentials during famine and plague events in medieval London, while controlling for missing data. The results suggest higher risks of famine and plague mortality for males and for individuals previously exposed to stressors, and higher risks of plague (but not famine) mortality for older adults. Further, we find evidence that protein-rich diets were protective against famine and plague mortality. Our findings highlight how various biological and social factors shaped risks of mortality in medieval London, even in the context of major mortality crises, which are often assumed to be indiscriminate in nature.