The recent pandemic has considerably changed urban transportation while highlighting the weaknesses of the current transport modes. The crisis provided a unique opportunity to redesign the urban mobility plans in a more sustainable and resilient way. This study captured the impact of the COVID-19 outbreak and the subsequent restrictive measures on citizens’ commuting habits and travel mode choice in two Cretan cities with academic communities and intense seasonality of tourism, in two phases (four periods) before, during, and after the quarantine. The sample consisted of 308 (1st phase) and 193 (2nd phase) citizens, 60% and 30% permanent residents of Chania and Rethymno, respectively. During the weeks before the pandemic, 4/10 participants opted for travelling by car daily, either as a driver or as a passenger; almost the same ratio chose walking; 1/10 used public transport (bus). During the first week of the quarantine, one-quarter had decreased car usage and opted for sustainable transport modes (walking, cycling, public transport). The population who chose walking 1-2 times weekly almost doubled. Nevertheless, most factors were found to affect men and women differently; personal safety and road safety are significantly more important for women; ecological footprint is a less essential parameter for men’s travel mode choice. Private vehicle use still holds a considerable role in urban transportation, and noteworthy is due to the sharp decline in public transit in January-February and April and the meager percentage of public transport ridership (1%). The analysis and modelling could be useful in the future design of more sustainable and resilient mobility strategies.