The unprecedented restrictions imposed due to the COVID-19 pandemic, including movement control orders and lockdowns, altered our daily habits, and severely affected our well-being and physiology. The effect of these changes is yet to be fully understood. Here, we analyzed highly detailed data on 169 participants for 2-6 months, before and during the second COVID-19 lockdown in Israel. Our entire study was conducted during the COVID-19 pandemic, and therefore is the first to decipher the specific effects of the lockdown from the general effects of the pandemic. We extracted 12 well-being indicators from sensory data of smartwatches and from self-reported questionnaires, filled on a daily basis using a designated mobile application. We used a mixed ANOVA model to study the interplay between age, gender, and chorotype on well-being before and after lockdowns. We found that at the population level, lockdowns resulted in significant changes in mood, sleep duration, sport duration, social encounters, resting heart rate, and the number of steps. The lockdown's adverse effects were greater for young early chronotypes who did not increase their sleep duration, reduced activity level and suffered from significantly reduced mood, and for women, who further suffered an increase in stress levels and a greater decline in social encounters. Our findings underscore that while lockdowns severely impacted our well-being and physiology in general, greater damage has been identified in certain subpopulations. Based on the observed effects, special attention should be given to younger people, who are usually not in the focus of social support, and to women.