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<b>Background:</b> The post-acute sequelae of SARS-CoV-2 infection represent a growing public health concern. While associations between COVID-19 and metabolic disorders have been reported, less is known about this risk in young, healthy populations. This study aimed to quantify the risk of developing new-onset metabolic disorders following SARS-CoV-2 infection among U.S. active-duty service members. <b>Methods:</b> We conducted a propensity score-matched cohort study using U.S. Military Health System data between July 2020 and June 2021 of active-duty service members (ADSM) aged 18 to 65 years old. COVID-19 infections were identified through ICD-10 codes or laboratory results. A 1:2 matched cohort compared 103,789 COVID-19 exposed individuals with 207,578 controls. Outcomes included incident diagnoses of type 2 diabetes mellitus (T2DM), hypertension (HTN), hyperlipidemia (HLD), metabolic dysfunction-associated steatotic liver disease (MASLD), and metabolic syndrome (MetS) within one year. Cox proportional hazards models calculated adjusted hazard ratios (aHR) while controlling for obesity and overweight status. <b>Results:</b> The median age for both those with and without COVID-19 infection was 26 years (interquartile range 22-33 years), with males comprising the majority of participants (81.1% male, 18.9% female). COVID-19 infection was associated with significantly increased hazards for incident HTN (aHR 1.09; 95% CI, 1.01-1.18), HLD (aHR 1.30; 95% CI, 1.10-1.54), and MASLD (aHR 1.36; 95% CI, 1.15-1.60). However, no significant increased risk was observed for T2DM or MetS. <b>Conclusions:</b> COVID-19 infection was associated with significantly increased risk of developing HTN, HLD, and MASLD, highlighting important long-term metabolic consequences in a young, healthy population.