Purpose <p>Emerging evidence suggests associations between gut microbiota patterns and autism-related behavioral and gastrointestinal features, increasing interest in probiotic interventions. This trial aimed to evaluate the effects of kefir-derived probiotics (K11 and K11-TMAX) on adaptive functioning, autism-related traits, and inflammatory/metabolic markers in children with Autism Spectrum Disorder (ASD).</p> Methods <p>In this parallel double-blind randomized clinical trial, 182 children with ASD (3–11 years) were randomly assigned (1:1:1) to the placebo, K11, or K11-TMAX groups. Assessments were conducted at baseline, day 45, and day 90. The primary outcome was the change in the Vineland-3 Adaptive Behavior Composite. The secondary outcomes included the Autism Diagnostic Observation Schedule (ADOS-2) Calibrated Severity Score (CSS), the Childhood Autism Rating Scale (CARS), inflammatory/metabolic biomarkers (insulin, C-reactive protein, prolactin, serum cortisol, and fecal calprotectin) and the fecal microbiota (Colony-Forming Units [CFUs] of <i>Lactobacillus</i> spp. and <i>Escherichia coli).</i> Randomization was computer-generated, and participants, caregivers, and outcome assessors were blinded.</p> Results <p>A total of 182 children was randomized to placebo (<i>n</i> = 57), K11 (<i>n</i> = 65), or K11-TMAX (<i>n</i> = 60) groups. On Day 90, participants in the K11 and K11-TMAX groups showed significant within-group improvements in Vineland-3 Adaptive Behavior Composite (<i>p</i> &lt; 0.05), with consistent changes across domains. The number of participants analyzed for the primary outcome was 182 (100%). No statistically significant between-group differences were detected. The secondary outcomes included reductions in the ADOS-2 and CARS scores in the probiotic groups. Biomarker analyses revealed decreases in insulin, C-reactive protein, and cortisol in both probiotic groups, with an additional reduction in fecal calprotectin in the K11-TMAX. Fecal microbiota analysis revealed a significant increase in <i>Lactobacillus</i> spp. and a concomitant reduction in <i>Escherichia coli</i> in the probiotic groups. The reported adverse events were mild and generally similar across groups; no severe or treatment-related events were identified.</p> Conclusion <p>K11 and K11-TMAX supplementation was associated with within-group improvements in adaptive functioning and autism-related traits over 90 days, without statistically significant between-group differences; findings justify larger, longer trials powered for between-group effects.</p> Level of evidence <p>Level I- randomized controlled trial.</p> Trial registration <p>ClinicalTrials.gov Identifier: NCT06382909 (<a href="https://clinicaltrials.gov/study/NCT06382909">https://clinicaltrials.gov/study/NCT06382909</a>). Registration date: March 28, 2024.</p>