How Running Might Hurt Your Gut and How to Fix It. Running comes with many benefits, which includes shedding excess weight off of the waist. While you may look good on the outside from running, your gut may not be feeling the best on the inside. Vigorous exercise like running can cause those with sensitive GI tracts to flare up with issues. Runner’s gut is real, and it can have you diverting from the finish line to the bathroom stall.…