BackgroundAutistic children experience disproportionately high rates of malnutrition compared to non-autistic (NA) peers. Sensorimotor integration differences (SMD), prevalent in 69–95% of autistic individuals, are hypothesized to drive this disparity. SMD contributes to core autistic traits that exacerbate feeding difficulties (e.g., food selectivity), potentially leading to malnutrition and gut dysbiosis. Current caregiver-reported SMD assessments lack validity in autistic populations and are prone to cultural and socioeconomic biases, limiting insight into nutritional outcomes.ObjectiveTo investigate relationships between objectively measured SMD, dietary patterns, nutritional status, and gut microbiota composition in autistic children versus NA peers.MethodsThis comparative cross-sectional study will recruit 100 autistic children and adolescents (aged 3–17 years) and 200 age-/sex-matched NA peers (including 100 with developmental disorders other than autism). Autism severity will be assessed using the Childhood Autism Rating Scale; NA peers will be screened with the Autism Spectrum Quotient-10. Dietary intake will be evaluated via three 24-hour dietary recalls, supplemented by questionnaires on socioeconomic status, health, and medications. Nutritional status (anthropometry, bioimpedance) and gut microbiota composition and diversity will be assessed. SMD proxies (sensory gating, sensory adaptation) will be measured using a smartphone application.AnalysisGroup comparisons will employ multivariate regression models, adjusting for age, sex, socioeconomic status and medication use. We hypothesize significant between-group differences in dietary patterns, nutritional status, microbiota profiles, and SMD measures. Objectively measured SMD in autistic children and adolescents is expected to correlate with symptom severity, dietary patterns, and differences in microbiota composition and diversity.Ethics and disseminationThe study has been approved by the Escuela Superior Politécnica de Chimborazo Ethics Committee (Ref: IO-01-CEISH-ESPOCH-2025). All participants will receive personalized nutritional counseling. Findings will be disseminated through peer-reviewed open-access publications, scientific conferences, and community workshops.