Background/Objectives: A lifelong gluten-free diet (GFD) is the only treatment for celiac disease (CD). However, current methods for monitoring GFD adherence do not accurately assess gluten exposure. Stool detection of gluten immunogenic peptides (GIP) may provide an objective tool for detecting recent gluten exposure. The aim of this study was to evaluate stool GIP detection, compared with serology and the validated Biagi dietary questionnaire, for monitoring GFD adherence in children with CD. Methods: In this prospective multicenter study, pediatric patients with CD on a GFD for at least 1 year were enrolled. Serum and stool samples were collected on the same day to assess serum anti-transglutaminase (TTG) and anti-endomysium (EMA) antibodies and stool GIP. Patients also completed the Biagi dietary questionnaire. Results: Forty-one pediatric patients with CD on a GFD for a median of 6.5 years were enrolled. Serum TTG and/or EMA were positive in 8/41 patients (19.5%), Biagi questionnaire identified 8/41 patients (19.5%) as non-adherent, whereas stool GIP was positive in 17/41 (41.5%). Combining serology with the dietary questionnaire increased the proportion of non-adherent patients to 34%. Adding stool GIP detection increased this proportion to 51% and 46% when combined with serology or the dietary questionnaire, respectively. Overall, 23/41 patients (56%) showed evidence of gluten exposure when positivity in at least one of the three methods was considered. Conclusions: A high rate of recent gluten exposure was detected in children with CD on a long-term GFD. Stool GIP detection may provide complementary information to conventional methods for monitoring GFD adherence and may help identify patients requiring further dietary assessment or intervention.