Urban areas have been dramatically impacted by the sudden and fast spread of the COVID-19 pandemic. As one of the most noticeable consequences of the pandemic, people have quickly reconsidered their travel options to minimize infection risk. Many studies on the Bike Sharing System (BSS) of several towns have shown that, in this context, cycling appears as a resilient, safe and very reliable mobility option. Differences and similarities exist about how people reacted depending on the place being considered, and it is paramount to identify and understand such reactions in the aftermath of an event in order to successfully foster permanent changes. In this paper, we carry out a comparative analysis of the effects of the pandemic on BSS usage in two French towns, Toulouse and Lyon. We used Origin/Destination data for the two years 2019 (pre-pandemic) and 2020 (pandemic), and considered two complementary quantitative approaches. Our results confirm that cycling increased during the pandemic, more significantly in Lyon than in Toulouse, with rush times remaining exactly the same as during the pre-pandemic year. Among several results, we note for example that BSS usage is more evenly spread throughout the day in 2020, peripheral/city center flow is more noticeable in Toulouse than in Lyon and that student BSS usage is more specific in Lyon. We also found that trip duration during the pandemic situation was longer on working days and shorter on weekends.