A few years after the start of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, scientific understanding of COVID-19’s etiopathogenesis expanded significantly. However, further efforts are needed to unravel the pathophysiological mechanisms of long COVID syndrome. According to the World Health Organization, this condition arises within 3 months of SARS-CoV-2 infection and persists for at least 2 months; it occurs more often in people who have developed severe COVID-19 and in unvaccinated people than in vaccinated people. The clinical manifestations vary from general symptoms, such as tiredness and worsening of the perception of health, to disorders of a specific organ involved, such as endocrine, neurological, psychiatric, and gastrointestinal disorders. This entry initially describes the early COVID-19’s impact on new-onset pathologies and mental disorders and, subsequently, focuses on gastrointestinal and hepatic disorders as consequences of COVID-19, also considering the progress in our understanding of microbiota-gut-brain and liver-brain interactions. The paper also provides an overview of the COVID-19’s impact on the hepatitis C virus therapy during the era of direct acting antivirals.