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The aim of this study is to examine how physical performance has changed after 15 weeks (109 days) long-term absence of organized training in youth soccer players imposed by the stay at home orders. A total of sixty-eight young male soccer players from different age categories (U15, U16, U17 and U19) voluntarily participated in the prospective cohort study. Body fat percentage (BF%), counter-movement jump (CMJ), 30 m sprint, change-of-direction (COD) and yo-yo intermittent recovery test level-1 (YYIRTL-1) were evaluated twice (before and after the detraining period). Subsequently, 2 × 2 repeated measures ANOVA was used to investigate group and time differences in repeated measurements. A significance level of p < 0.05 was implemented. CV and SWC values were calculated to test the reliability of the tests performed at different times. Statistical analysis was performed using the IBM SPSS statistics software (v.25, IBM, New York, NY, USA). Significant increments in BF%, 30 m sprint, and COD (left and right), and also significant decrements in CMJ and YYIRTL-1, were found after the detraining period. A long-term detraining period due to the stay at home orders has a detrimental effect on body composition, neuromuscular performances, and aerobic capacity in youth soccer players.