This paper evaluates gender inequality in employment risks during the first and the second wave of the COVID-19 pandemic in Germany. We use individual-level panel data collected weekly between 20 March and 9 July 2020, and again in January 2021, to examine the risks of short-time work, job loss and unpaid furlough, as well as having to work on-site by means of growth curve modelling. The results reveal gender inequality in employment risks and gendered use of governmental support schemes. During the early phase of the pandemic, women had a higher probability of being temporarily exempted from work, but a lower probability of being in short-time work and receiving the associated state benefits. Compared to men, women also continuously had a higher probability of working on-site rather that from home. Consequently, women’s employment during the pandemic is more polarized between job loss or working on-site with the associated infection risk. Gender inequalities are rooted in the long-term gendered dualization of the German labour market with the low-wage sector and marginal employment being female dominated. The results call for close monitoring of long-term gendered effects of the pandemic recession and an adjustment of governmental crisis measures to the requirements of the female workforce.