Background and Aim Because acute infectious gastroenteritis may cause post‐infection irritable bowel syndrome and functional dyspepsia and the severe acute respiratory syndrome coronavirus‐2 affects gastrointestinal (GI) tract, coronavirus disease‐19 (COVID‐19) may cause post‐infection‐functional GI disorders (FGIDs). We prospectively studied the frequency and spectrum of post‐infection‐FGIDs among COVID‐19 and historical healthy controls and the risk factors for its development. Methods Two hundred eighty patients with COVID‐19 and 264 historical healthy controls were followed up at 1 and 3 months using translated validated Rome Questionnaires for the development of chronic bowel dysfunction (CBD), dyspeptic symptoms, and their overlap and at 6‐month for IBS, uninvestigated dyspepsia (UD) and their overlap. Psychological comorbidity was studied using Rome III Psychosocial Alarm Questionnaire. Results At 1 and 3 months, 16 (5.7%), 16 (5.7%), 11 (3.9%), and 24 (8.6%), 6 (2.1%), 9 (3.2%) of COVID‐19 patients developed CBD, dyspeptic symptoms, and their overlap, respectively; among healthy controls, none developed dyspeptic symptoms and one developed CBD at 3 months (P