ObjectiveThe coronavirus disease 2019 (COVID-19) pandemic has impacted everyone, but there are few data regarding how the pandemic has influenced the lives of children with gastrointestinal (GI) conditions. This cross-sectional study assessed pandemic-related social disruption (PRSD) in children with inflammatory bowel disease (IBD), celiac disease (CD), and irritable bowel syndrome (IBS), and the potential buffering effect of the parent–child relationship.MethodsA survey completed between September and December 2020 asked 146 children (ages 8–17) diagnosed with IBD (n = 44), CD (n = 81), or IBS (n = 51) and 185 parents how the pandemic has contributed to social disruption (i.e., financial stability, COVID-19 exposure, school changes, GI needs, and isolation) and their social–emotional well-being. Structural equation modeling was used to examine the role of social disruption on well-being, and the moderating effect of the parent–child relationship.ResultsIncreased social disruption predicted worse parent, β = 0.24, p = .02, and child well-being, β = 0.38, p < .01. The parent–child relationship moderated the relationship between parent and child well-being, β = 0.21, p = .03. Strong parent–child relationships predicted a positive association between parent and child well-being, β = 0.23, p = .003, whereas medium, β = 0.09, p = .14, and poor, β = −0.06, p = .52, relationships did not.ConclusionsPRSD negatively impacted the well-being of children with GI conditions, and the parent–child relationship moderated this relationship. These findings are relevant to pediatric psychologists treating the physical and mental health needs of children with GI conditions and their parents.