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The long-term health implications of COVID-19 have posed a new challenge in clinical management, especially with the appearance of long COVID syndrome. Most of the attention has been on respiratory and neurological sequelae, but its impact on GI health is underexplored. It has been observed that abnormalities detected during the acute phase of SARS-CoV-2 infection can be used to predict potential post-acute sequelae within the digestive system. These anomalies are accompanied by immune dysregulation, cytokine storms, and damage to hepatocytes, resulting in fatigue, loss of appetite, and nutritional deficiencies persisting for several months and, therefore, significantly worsen recovery and quality of life. This current letter addresses the pertinent interaction between liver dysfunction and GI symptoms in the context of long COVID, highlighting the urgent need for early detection and personalized therapies in predisposed patients. It also examines the influence of vaccination, metabolic health, and early nutrition supplementation on the development and progression of these sequelae. Recent research emphasizes the increasing importance of gut dysbiosis and its link to hepatic impairment in long-term COVID patients. This letter underscores the importance of interdisciplinary collaboration and highlights the urgent need for conducting more research on GI manifestations of long COVID in order to define the mechanisms involved and possible pathways toward therapy.