The average time it takes to fully digest food from when you eat it to when it exits your body varies from person to person. It can take anywhere up to two to five days to fully digest food you have eaten. Medical conditions, such as irritable bowel syndrome (IBS), gastroparesis (the stomach takes longer to empty), inflammatory bowel disease, or functional dyspepsia (indigestion) can affect how food moves through your digestive system, thus altering the transit time.