Introduction: Autism spectrum disorder (ASD) comprises a group of developmental disorders characterized by deficits in social interaction and behavioral patterns. Children with ASD may face nutritional challenges, primarily due to their restrictive behaviors and frequent gastrointestinal issues. Objective: The objective of the present study was to assess nutritional status, dietary habits, and intestinal permeability in a sample of individuals with ASD. Methods: A cross-sectional study was conducted with 24 children and adolescents (both sexes), aged 4 to 18 years, living in two cities of Mexico (Aguascalientes and Querétaro). Weight and height were measured, and body mass index for age was calculated and compared using WHO Z-scores. Diet was assessed through three 24 h dietary recalls and a food frequency questionnaire. Intestinal permeability was evaluated using a lactulose/mannitol test by HPLC. Results: A high prevalence of malnutrition was observed; 12.5% of the participants were underweight, and 45.8% were overweight or obese. Children had a low intake of fiber, vitamin E, folate, potassium, zinc, and phosphorus and a high intake of sodium. On average, the intestinal permeability ratio was 0.09 ± 0.05, with 54.2% of the children exhibiting high intestinal permeability. Conclusions: It is advisable to develop food counseling strategies for children with ASD to prevent micronutrient deficiencies, promote healthy weight, and improve gastrointestinal integrity.