A gluten-free diet (GFD) is the only treatment available for celiac disease (CD); hence, it is important to ensure correct adherence to the diet and adequate monitoring of the diet. The present study aims to assess the importance of an early follow-up of celiac patients after diagnosis of the disease, identify the role of stool gluten immunogenic peptides (GIPs) in the assessment of GFD adherence, and analyze possible nutritional imbalances or deficiencies in the GFD. This is a cross-sectional study carried out in pediatric patients with newly diagnosed CD in a tertiary hospital in Spain. Of the 61 patients included, 14% had positive stool GIPS at 4 months after CD diagnosis, Among them, 88% had negative stool GIPS at 9 months after diagnosis, following dietary advice. We found nutritional deficiencies in the GFD, such as vitamin D (with only 27% of patients with adequate intakes), folate, calcium, magnesium, and fiber. Similarly, we found imbalances: excess protein and fat intakes and a high percentage of total daily energy intake came from ultra-processed foods (UPF). These findings emphasize the importance of early follow-up of children after diagnosis of CD. It is also crucial to identify patients with poor GFD compliance based on stool GIPS and analyze GFD nutritional imbalances and deficits. Our findings may contribute to the development of specific strategies for the early follow-up of patients with CD, including appropriate nutritional counselling.