Gut microbiota alterations play a key role in the pathogenesis of inflammatory bowel disease (IBD), and its modification through specific diets is an emerging line of treatment that is currently being researched. The aim of this study was to assess changes in the dietary habits of patients with Crohn’s disease (CD) and their long-term adherence to dietary therapy with the Crohn’s disease exclusion diet (CDED) after one year. To analyse the modification of dietary habits and adherence to the Mediterranean diet (DM), the KIDMED questionnaire, a food consumption frequency questionnaire, was used. Twenty-four hour recalls at two timepoints, namely prior to the start of the dietary therapy and one year later, were also carried out. The processing degrees of the foods consumed by the patients were analysed at both timepoints using the NOVA classification system. Data from 24 patients (15 boys), with a mean age of 12.7 ± 2.9 years at the start of the dietary therapy, were analysed. All patients showed an improvement in their dietary pattern in the form of a reduction in the intake of ultra-processed foods (UPFs); a higher adherence to the MD; a decrease in the intake of cold meats, seafood, pasta, precooked foods, soft drinks, and pastries; an increase in the intake of eggs, legumes, dairy products, and nuts (p < 0.05); and adequate adherence, even in the long-term, to foods allowed during the different phases of the dietary regimen. Although more factors have an impact on the course of the disease in these patients, improving their dietary habits is essential.