Due to the characterization of Autism Spectrum Disorder (ASD) as a multifaceted syndrome, most diagnoses are still not precise. To avoid pharmacological treatments, natural strategies with significant potential to reduce oxidative stress are sought. This study aims to identify the influence of quercetin on oral and gut microbiota, as well as evaluate the action of this bioactive compound in relation to the signs and symptoms that characterize ASD individuals. This research, that is a systematic review, was conducted on the PubMed platform from 2014 to 2024. The keywords used were: “quercetin and autismo”; “autism, quercetin and antioxidante”; “quercetin and oral microbiota”; “quercetin and intestinal microbiota.” Evidences showed that quercetin reduces oxidative stress under various conditions, both in vitro and in vivo, indicated mitochondrial function optimization and protection against xenobiotic-induced damage. It demonstrated benefits such as improved cognitive function, reduced blood glucose levels, and activation of the SIRT1 enzyme. It preserved oral microbial diversity and reduced the dominance of inflammatory taxonomic groups. It positively influenced the gut microbiota by decreasing Firmicutes and increasing Bacteroidetes. This could represent a novel approach to conditions related to the gut-brain-microbiota axis. Studies suggest that quercetin offers a promising approach to mitigate physiological manifestation challenges, improve inflammatory responses, act as a potent antioxidant, and modulate oral and gut microbiota. It is hoped that attention to these individuals will continue to grow progressively.