Background & aims: Emergency measures in the face of the recent COVID-19 pandemic have been different among countries, although most have opted for confinement and restrictions on social contact. These measures have generated lifestyle changes with potential effects on individuals' health. The disturbances in daily routines due to confinement and remote work have impacted circadian rhythms and energy balance; however, the consequences of these disruptions have not been studied in depth. The objective was to evaluate the impact of 12-week confinement on body weight, considering changes in several external synchronizers of the biological clock. Methods: The participants, 521 university students (16–35 years), responded to 52 questions oriented to determine light exposure, sleep patterns, sedentary lifestyle, and eating times. Results: We found a reduction in sunlight exposure and sleep duration, an increment in sedentarism and screen exposure, and a delay in the timing of the main meals and sleep in the whole cohort. These behavioral changes were associated with a twofold increase in obesity. Subjects who increased their sedentary hours and shortened their sleep to a higher degree were those who gained more bodyweight. The most influential factors in body weight variation during confinement were sleep duration, physical activity (sedentarism), and light (timing of screen exposure). The mediation model explained 6% of the total body weight variation. Conclusions: Results support a significant impact of confinement on several external synchronizers of the biological clock and on body weight. Health-related recommendations during the pandemic must include behavioral recommendations to mitigate the adverse effects on the biological clock.