BackgroundAcute gastrointestinal infections can lead to post-infectious irritable bowel syndrome (PI-IBS). Moreover, coronavirus disease (COVID-19) is related to long-term gastrointestinal sequelae. In this study, the frequency, disease spectrum, and risk factors for post-infection functional gastrointestinal disease (PI-FGID) in COVID-19 patients and healthy controls were prospectively examined.MethodsValidated Rome III and Rome IV questionnaires and limited objective assessment were used to assess the incidence of PI-FGID in 190 COVID-19 patients, and 160 healthy controls prospectively followed for 1, 3, and 6 months.ResultsSix(3.2%), 1(0.5%), 3(1.6%), 5(2.6%), 6(3.2%)COVID-19 patients had diarrhea, abdominal pain, constipation, dyspepsia and their overlap at 1 month, respectively, while 4(2.1%), 1(0.5%), 4(2.1%), 4(2.1%), and 6(3.2%)COVID-19 patients had diarrhea, abdominal pain, constipation, dyspepsia and their overlap at three months, respectively. Furthermore, 2(1.3%), 4(2.5%), and 3(1.9%)healthy controls developed constipation, dyspepsia, and their overlap at one month, respectively (P= 0.193), while 2(1.3%), 4(2.5%), and 2(1.3%)healthy controls developed constipation, dyspepsia and their overlap at three months, respectively (P= 0.286). FGIDs incidence was higher among COVID-19 patients(8.9%) than in healthy controls(3.1%) at 6-month follow-up (P= 0.025). Moreover, 7 (3.7%), 5 (2.6%), 3 (1.6%), and 2 (1.1%) COVID-19 patients developed IBS, functional dyspepsia(FD), functional diarrhea(FDr), functional constipation(FC)at six months, respectively, while only 2 (1.3%) and 3 (1.9%) healthy controls developed IBS and FD at six months, respectively. Notably, gastrointestinal(GI)symptoms at onset were the independent risk factors for post-COVID-19 FGIDs at six months.ConclusionsCOVID-19 increases new-onset PI-FGID at six months compared with healthy controls. GI symptom at the onset of COVID-19 is an independent risk factor for post-COVID-19 FGIDs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-023-08401-x.