The present study compared changes in body composition during the COVID-19-associated lockdown with the same period of the following season in elite soccer players. Fifteen elite male soccer players (30.5 ± 3.6 years.) underwent a bioelectrical impedance analysis (BIA) before (end of February) and after (end of May) the lockdown, which occurred during the 2019/2020 season, and at the same period during the following competitive season in 2020/2021, when restrictions were lifted. Fat and muscle mass were estimated using predictive equations, while phase angle (PhA) and bioelectrical impedance vector analysis (BIVA) patterns were directly measured. After lockdown, fat mass remained unchanged (p > 0.05), while muscle mass (95%CI = −1.12/−0.64; ES = −2.04) and PhA (95%CI = 0.51/−0.24, ES = −1.56) decreased. A rightward displacement of the BIVA vector was also found (p < 0.001, ES = 1.50). After the same period during the regular season, FM% and muscle mass did not change (p > 0.05), while the PhA increased (95%CI = 0.01/0.22; ES = 0.63). A leftward vector displacement (p < 0.001, ES = 1.05) was also observed. The changes in muscle mass correlated with changes in PhA (“lockdown” season 2019/2020: ß = −1.128, p = 0.011; “regular” season 2020/21: ß = 1.963, p = 0.011). In conclusion, coaches and strength conditioners should monitor muscle mass in soccer players during detraining periods as this parameter appears to be mainly affected by changes in training plans.