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Every other day I ride a bike for 40 minutes maintaining a cadence of at least 90 and work up quite a sweat. After that I do weights for about an hour changing muscle groups every time. I usually rest about 15-20 minutes after the bike ride. Would if make a difference if I drank the protein shake after the biking and before weights or go ahead and wait till after i do weights?

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Not a huge difference, but that's a lot of aerobic activity before weight training. If anything, I'd recommend some carbs to replenish glycogen stores. There's also no reason the protein couldn't be consumed during weight training.

It depends on what your goals are, but here's a representative article that might make you reconsider the order in which you do things.

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