There is still controversy surrounding the effectiveness of dietary interventions for autism spectrum disorder (ASD), namely the gluten-free/casein free diet and the ketogenic diet. Additionally, as studies mainly investigated their impact on ASD symptoms and behaviors, much remains unknown about their mechanisms of action and physiological effects. Given the recent surge of global interest in the gut-brain axis and its involvement in ASD, we underline the importance of understanding the physiological effects of such restrictive diets that remove certain nutritional items from one's diet. Some evidence has emerged with findings of the gut microbial, inflammatory, and neuronal effects of these diets. We propose probiotics as a potential alternative that can serve similar biological purposes as these elimination diets and outline different physiological routes whereby probiotics can lead to improvements for individuals with ASD. We hope that future research can delineate the complete physiological effects of these diets. Such knowledge can guide the creation of more informed interventions, which conserve the components resulting in positive behavioral change while being less restrictive and devoid of the harmful effects of limiting certain nutrients.