A case report of COVID-19 infection in a patient presenting with upper and lower gastrointestinal and respiratory symptoms, ending in respiratory failure and the need for invasive mechanical ventilation, presenting with improvement in his respiratory and gastrointestinal symptoms, but with limitations for extubation due to altered state of consciousness despite weaning from analgesia for more than 72 hours, in whom elevated levels of ammonia were found without signs of liver failure. Diarrhoea and liver involvement are frequent manifestations in patients with COVID-19, which can possibly lead to a decrease in carnitine levels and secondary hyperammonaemia, becoming a challenge for clinicians.