Most supplements are safe to take during the protocol.
Ones that are not may contain problem fillers, or be oil based. Tiny oil capsules like Vitamin D are not a problem, but if you take a big handful of those huge fish oil caps, it could cause gains or stalls, and could affect your ability to stabilize later. Don't worry about small amounts of dry fillers like rice flour. Its not enough to make a difference, and there is a little starch in the protocol menu anyway.
I was very cautious in my early rounds not to take any additional hormones such as DHEA and even stopped by thyroid meds. In my last couple rounds, I didn't stop any of my supplements or my thyroid med. My only change was to replace a couple of the oil-carried ones with a powdered version. There was no difference in losses or pattern of losses.
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