It is unclear how the COVID-19 pandemic has impacted children with gastrointestinal conditions. This cross-sectional study assessed the impact of social disruption from the pandemic on children with gastrointestinal conditions, and the potential moderating effect of the parent-child relationship. An online survey completed between September - December 2020 asked 185 parents and 146 of their children (ages 8-17) diagnosed with IBD (n = 44), celiac disease (n = 81), and IBS (n = 51) how the pandemic has contributed to social disruption, and child and parent well-being. Increased social disruption predicted worse parent and child well-being. The parent-child relationship moderated the relationship between parent and child well-being, with strong relationships predicting a positive association between parent and child well-being. Social disruption has significantly impacted the well-being of children with gastrointestinal conditions during the pandemic.