Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental condition often accompanied by metabolic and nutritional imbalances. Conventional dietary interventions, such as the gluten-free, casein-free diet, typically fail to consider individual genetic variations. Nutrigenomics, the study of gene-nutrient interactions, offers a promising framework for exploring personalized dietary interventions that may help address the metabolic and neurological complexities associated with ASD, although current evidence remains preliminary. This research note offers recommendations for integrating nutrigenomics into special education through a multidisciplinary approach that combines clinical nutrition, genetics, and educational practice via a 3-phase agenda. Stage 1 focuses on identifying behavioral subgroups within special education settings and using validated tools such as the Child Behavior Checklist Scale to analyze nutritional intake. Stage 2 involves the development and pilot-testing of behavior-specific nutrition protocols that are tailored to these subgroups, incorporating input from practice experts in nutrigenomics. Lastly, in Stage 3, a personalized nutrition model that incorporates genetic screening and metabolic profiling is constructed in collaboration with dietitians, educators, and caregivers. By bridging clinical and educational domains, this study seeks to establish nutrigenomics-based nutrition therapy as a viable and equitable intervention for improving health and developmental outcomes among students with ASD.