Background: The COVID-19 pandemic posed unprecedented challenges for elite athletes, disrupting training routines and affecting mental health. This study examined the impact of social isolation on training, sleep, motivation, and psychological well-being among Portuguese Paralympic athletes. Methods: Forty-five athletes (31.36 ± 10.81 years) from the Paralympic Preparation Program participated, divided into the Paralympic Preparation Project (PPP; n = 21) and the Paralympic Hopes and Talents Project (PHTP; n = 24). Training routines before and during social isolation were compared. Sleep duration, training motivation, and mental health were assessed using the Mental Health Inventory-5 (MHI-5). The analysis employed paired and independent t-tests and a multiple linear regression (Enter method) to examine predictors of mental health. Results: Daily training duration declined by 34.3% (p < 0.001), though weekly frequency remained stable (p = 0.061). PPP athletes reported higher mental health scores than PHTP athletes (66.24 vs. 60.37; p = 0.048). The regression model explained 42.8% of the variance in mental health (R2 = 0.428). Sleep duration was positively associated with mental health and showed the highest standardized coefficient in the regression (ß = 0.351; p = 0.008), followed by PPP status (ß = 0.315; p = 0.024) and motivation (ß = 0.278; p = 0.041). Conclusions: Maintaining biological routines, particularly sleep and motivation, supports mental health under social isolation. Higher well-being among PPP athletes underscores the need for targeted interventions for less experienced athletes. Sports organizations should prioritize sleep hygiene and psychological support to mitigate vulnerability during crises.
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