Research on clinical prognostic risk factors in coronavirus disease 2019 (COVID-19) is still ongoing to shed light to the pathogenesis and the treatment of viral infections. Coenzyme Q10, which is an important antioxidant that plays a role in energy conversion and adenosine triphosphate (ATP) production, has been suggested as one of the targets of COVID-19. In our study, we aimed to investigate the effects of serum coenzyme Q10 levels on survival and clinical prognosis in critically ill COVID-proven and COVID-suspected patients. After ethics committee approval, adult patients who were admitted to COVID intensive care unit (ICU) between 1^st January 2021 and 1^st January 2022 were included into the study. Patients were divided into two groups: those whose four consecutive polymerase chain reaction (PCR) results were negative and whose clinical symptoms could be explained by another pathology constituted the COVID-negative control group, and patients with positive PCR results constituted the COVID-positive group. Demographic data, comorbidities, admission symptoms, Acute Physiology and Chronic Health Evaluation II (APACHE-II) and Sequential Organ Failure Assessment (SOFA) scores, length of stay (LOS), laboratory results, mechanical ventilation (MV) and vasopressor (VP) requirement, and mortality of the patients were recorded prospectively. Serum coenzyme Q10 levels were measured at ICU admission and weekly afterward with high-performance liquid chromatography (HPLC) method. COVID-positive group had 96 and COVID-negative group had 62 patients. The COVID-positive groups had higher median serum coenzyme Q level at admission than the negative group (p = 0.022). No significant relationship was found between serum coenzyme Q10 values and length of ICU or hospital stay, SOFA or APACHE-II values, duration of VPs, need for renal replacement therapy (RRT), and survival analysis both in COVID-positive and -negative groups. When coenzyme Q10 levels at ICU admission were analyzed in all patients, the median coenzyme Q10 level was significantly higher in women than in men (1.28 vs 1.18 mg/L, p = 0.035). Patients with malignancy (p = 0.008), neurological disease (p = 0.038), or malnutrition (p = 0.001) had lower coenzyme Q10 levels than the patients without these clinical diagnoses. The presence of malnutrition increased the risk of mortality in the ICU [hazard ratio (HR): 3, 95% confidence interval (CI): 1.6–5.4, p < 0.001]. In conclusion, plasma coenzyme Q10 level alone cannot be a factor predicting mortality and morbidity in the COVID ICU patient group. However, low serum coenzyme Q10 level may be an important component of malnutrition, and malnutrition is one of the major risk factors of ICU mortality.