Coffee proved to be a strong trigger for increased intestinal permeability (leaky gut) for me. If you mix it with milk components that can cross the weakened intestinal wall (lactose, casein) problems arise. Do some self experimentation to see if this is the case with you too 1. try alcohol (another leaky gut trigger) and heavy cream 2. coffee with other types of milk (lactose free, youghurt, goat milk) to to see if your problem is linked to the lactose or casein content

Something to consider, apparently coffee has proteins that can trigger similar to gluten reactions: http://www.thehealthyhomeeconomist.com/gluten-issues-or-celiac-dont-drink-coffee/

Try doing a test on a empty stomach vs non-empty stomach.

If I drink coffee or milk after fasting, it seems to induce diarrhea after only 30 minutes, but if I have it with a big meal, or after eating recently, it doesn't bother me at all.

Coffee beans contain enzymes that irritate the entire digestive tract. Irritation results in inflammation and mucous production which can prevent the proper absorption of nutrients including carbohydrates. This can result in more food for the microbes in the colon resulting in what may appear to be symptoms of lactose intolerance. Ditch the coffee (chocolate too for the same reason) and see how things go. Additionally, if you are a regular alcohol drinker, you won't awaken with sufficient enzymes to digest the food you eat, so laying-off or severely restricting alcohol intake is a must for proper digestion.

I don't believe it's the coffee, I suffer exactly the same thing. The reason why I don't think it's the coffee is because I can drink coffee with soy milk (from the same cafe) and not have any reaction. I can have full cream or skim milk on my cereal, no reaction. I can drink instant coffee with half milk at home, no reaction. As soon as I have milk with coffee at a cafe I have a reaction? I've tried this at various coffee places over the years and the results are the same?