Several studies indicate that the situation of female researchers decreased disproportionally in comparison to their non-female colleagues. This paper examines which obstacles female researchers faced in their working life and how the working situation of researchers has changed during the COVID-19 pandemic. Germany and the UK were used to generate a sample of the two important European research intensive countries with different academic cultures. The ten highest ranked universities in both countries form the sample for an online survey of researchers in the field of social sciences. The paper provides results regarding the variance of productivity of female and non-female researchers during the pandemic and the relevant influencing factors on researchers scientific output in general. The analysis show that the pandemic has decreased the working conditions, as well as the scientific output, in the field of social sciences. Female researchers are affected by this trend slightly more than their non-female colleagues are. The pandemic also led to a shift in tasks performed, corresponding to increasing teaching and service-related tasks and decreased research related tasks. Furthermore, the results prove that individual characteristics, especially the fact of having children living in the household had a significant impact on the scientific output.