This population-based cohort study of 1,004 Swedish young adults found that BMI, body fat percentage, blood pressure, and pulse all increased significantly from the pre-pandemic period (2016–2019) to the COVID-19 pandemic period (2020–2021). Male sex, non-Scandinavian ethnicity, and pre-existing underweight or obesity were associated with greater increases in adiposity. Self-reported lifestyle changes, particularly decreased physical activity and increased sedentary time, were linked to adverse changes in body composition, highlighting the need for targeted public health interventions to prevent future non-communicable diseases.