Data from famines from the nineteenth century onward suggest that women hold a mortality advantage during times of acute malnutrition, while modern laboratory research suggests that women are more resilient to most pathogens causing epidemic diseases. There is, however, a paucity of sex‐disaggregated mortality data for the period prior to the Industrial Revolution to test this view across a broader span of history. We offer a newly compiled database of adult burial information for 293 rural localities and small towns in the seventeenth‐century Low Countries, explicitly comparing mortality crises against ‘normal’ years. In contrast to expected results, we find no clear female mortality advantage during mortality spikes and, more to the point, women tended to die more frequently than men when only taking into account those years with very severe raised mortality. Gender‐related differences in levels of protection, but also exposure to vectors and points of contagion, meant that some of these female advantages were ‘lost’ during food crises or epidemic disease outbreaks. Responses to mortality crises such as epidemics may shine new light on gender‐based inequalities perhaps hidden from view in ‘normal times’ – with relevance for recent work asserting ‘female agency’ in the early modern Low Countries context.