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A quick proof that the answer isn't "you poop it out": when you work out more, you don't poop more. (You do, however, breathe more, which points towards the correct answer.)

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Physical activity speeds up the digestive process, so you do often poop more when you work out.

... combined with the fact that many who work out heavily increase their caloric intake (eat more). :D

Some of it should be peed out.

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