The systematic review and meta-analysis included ten observational studies with a total of 232,448 participants. High consumption of ultra-processed foods (UPF) was significantly associated with a higher risk of irritable bowel syndrome (IBS) with an odds ratio of OR = 1.32 (95% CI: 1.16–1.49) based on 9 studies. It was also associated with a higher risk of functional dyspepsia (FD) with OR = 1.26 (95% CI: 1.07–1.49) based on 3 studies. The strongest association was shown for carbonated and sugar-sweetened snacks with OR = 1.98 (95% CI: 1.40–2.80). The finding for FD lost significance in the sensitivity analysis because it was influenced by one large cohort. Heterogeneity was low in studies with NOVA classification or comparison by quartiles (I² = 0%). Egger's test did not show significant asymmetry for IBS (p = 0.153). The conclusion recommends reducing UPF intake as a strategy to prevent IBS, for FD the evidence is preliminary.