Lifelong adherence to a gluten-free diet (GFD) is the cornerstone of management of celiac disease (CD), but adhering to a GFD can be hard. Although several factors are positively associated with adherence of pediatric CD patients to a GFD, it is unknown whether these are influenced by variability caused by the specific tool used to assess adherence to a GFD. Here, we aimed to evaluate how individual patient characteristics and dietary counselling by a trained dietitian influence adherence to a GFD in children with CD, as assessed by two validated questionnaires: the Biagi questionnaire and the Leffler short questionnaire adapted for pediatric patients. Some 139 children and adolescents were recruited in a cross-sectional, multicenter study. Concordance between the two questionnaires in defining adherence was fair (weighted Cohen’s kappa coefficient 0.39, 95%CI 0.19–0.60). Upon regression analysis, having a cohabiting family member with CD, being of Italian origin, and receiving specialized dietary counselling during follow-up were found to positively influence stricter adherence to a GFD for children with CD. Neither questionnaire detected a significant relationship between adherence to a GFD and the presence of symptoms after gluten ingestion. This study provides important new data on the factors influencing GFD adherence in the pediatric population, and highlights the importance of dietician input and overcoming language and cultural barriers when educating patients.