Brain-gut axis disorders, such as functional dyspepsia and irritable bowel syndrome (traditionally known as functional gastrointestinal disorders) have a prevalence of more than 10% in most countries and affect females more than males. In these disorders, visceral pain and motor alterations affecting the gastrointestinal tract are the key symptoms, together with psychoaffective alterations (depression, anxiety). Two general etiologies are generally recognized for their development: they may be caused by a local inflammatory or infectious problem in the gastrointestinal tract that sensitizes the visceral afferents and lead to consequent central hypersensitization; alternatively, they may develop associated to some kind of prolonged psychological stress in vulnerable people or vulnerable periods of life (i.e., due to early life stress). In recent years, studies have focused on the effects of coffee, its components (melanoidins) and its by-products (coffee spent grounds, coffee silver skin derivatives…) on the functions of the brain-gut axis, showing these products may cause subtle alterations in gastrointestinal motility, visceral sensitivity and behavioral parameters, in a sex-dependent manner. These effects need to be taken into account when new functional foods based on coffee and its by-products are to be developed for the general population. Considering the high prevalence of the brain-gut axis disorders, these effects need to be more deeply evaluated in relevant models.