Bodily self-consciousness, the state of mind that allows humans to be aware of their own body, forms the backdrop for almost every human experience, yet its underpinnings remain elusive. Here we combine an ingestible, minimally invasive capsule with surface electrogastrography to probe if gut physiology correlates with bodily self-consciousness in a sample of healthy men during a virtual bodily illusion. We discover that specific patterns of stomach and bowel activity (temperature, pressure, and pH) covary with specific facets of bodily self-consciousness (feelings of body location, agency, and disembodiment). These results uncover the hitherto untapped potential of minimally invasive probes to study the link between mental and gut states and show the significance of deep visceral organs in the self-conscious perception of ourselves as embodied beings.