During the 2020, the pandemic caused by the massive spread of the SARS-CoV-2 coronavirus (COVID-19) resulted in a global crisis. In Spain, the COVID-19 pandemic caused a lockdown for almost 100 days and forced the sudden stop of sport practices and competitions. This interruption had a negative impact on high-level athletes' mental health. However, its impact on young athletes, who are intrinsically developing a high-demanding dual career, remains unclear. Therefore, this study aimed at (1) describing and characterizing the general impact that COVID-19 lockdown had on Spanish young athletes' life-spheres and mental health, and (2) identifying different profiles of athletes regarding life-conditions and sport-related variables. A sample of 544 young athletes (M = 15.9; SD = 1.51) participated in this study. Measures included life-conditions and sport-related information along with the Holistic Monitoring Questionnaire (HMQ) and the General Health Questionnaire (GHQ-12). After the screening and description of the data, profiles were defined using a two-level cluster analysis using HMQ and GHQ-12 subscales. We explored differences in demographic and sports information between profiles using MANOVA and subsequent ANOVA. Results suggest a general negative impact of COVID-19 on young athletes' life-spheres and mental health, but with three different clusters regarding the degree of such impact. Cluster 1 grouped the 54.78% of the sample and exhibited a low negative impact of COVID-19 lockdown on life-spheres and few mental health issues. Cluster 2 grouped a 29.96% of the participants who reported a medium negative impact on life-spheres and moderate mental health issues. Cluster 3 represented 15.26% of the sample including participants who showed a high negative impact of the COVID-19 lockdown with high mental health issues. The paradigmatic participant in this third group would be a female student-athlete from a medium or low socioeconomic status with high academic demands and poor or inexistent training conditions during lockdown. Current findings emphasize the need to pay attention to young athletes' mental health and suggest possible influencing contextual variables. We suggest some applied recommendations aimed at helping clubs and sports institutions to mitigate the negative effects of such difficult circumstances on athletes' mental health.