Caffeine's most notable excretory effect is as a diuretic. It kicks the kidneys into overdrive, and you have to urinate more.
The effect on the bowels is less often noted, but stimulants in general can have an effect on the digestive tract. They have a stress effect on the brain, putting extra ephedrine/adrenaline into the blood stream, causing an increase in peristalsis.
The extreme version of this is the involuntary bowel-clearing of the flight-or-fight response. It is sometimes thought that this is a way to reduce weight in response to an emergency, though as with all "evolutionary" explanations it needs to be taken with a bit of salt. Either way, you're not getting all the way to panicky bowel-clearing here, just a bit of extra stimulation to the intestines moving your digestive tract forward faster.
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