Limosilactobacillus (L.; previously Lactobacillus) reuteri has been shown to influence gastrointestinal (GI) tolerance. This study was a secondary analysis of GI tolerance data from a multi-country, cross-sectional, observational study in healthy infants using the validated Infant Gastrointestinal Symptom Questionnaire (IGSQ) and a gut comfort questionnaire. Breastfed infants (BFI; n = 760) were compared to formula-fed infants receiving either L. reuteri-containing formula (FFI + LR; n = 470) or standard formula without any probiotic or prebiotic (FFI-Std; n = 501). The IGSQ composite scores (adjusted mean ± SE) in FFI + LR (22.17 ± 0.39) was significantly lower than in FFI-Std (23.41 ± 0.37) and similar to BFI (22.34 ± 0.30;), indicating better GI tolerance in FFI + LR than in FFI-Std. Compared with FFI-Std, FFI + LR had lower reports of difficulty in passing stools (11% vs. 22%; adjusted-odds ratio (OR) (95%CI) = 0.46 (0.31–0.68)), fewer hard stools (mean difference = −0.12 (−0.21, −0.02)) and less physician-confirmed colic (OR = 0.61 (0.45–0.82)), and similar to BFI. Parent-reported crying time (mean difference = −0.15 (−0.28, −0.01)), frequency of spitting-up/vomiting (mean difference = −0.18 (−0.34, −0.03)), volume of spit-up (mean difference = −0.20 (−0.32, −0.08)) and fussiness due to spitting-up/vomiting (mean difference = −0.17 (−0.29, −0.05)) were lower in FFI + LR versus FFI-Std and similar to BFI. In this study, L. reuteri-containing formula was associated with improved digestive tolerance and behavioral patterns.