What are the side-effects of Collagen Peptide? The most commonly reported side-effects of Collagen Peptide are nausea, pruritus, exanthema, gastrointestinal symptoms, and headache. The following is a list of possible side effects that may occur from the use of Collagen Peptide. This is not a comprehensive list. These side-effects are possible, but do not always occur. Some of the side-effects may be rare but serious. Consult your doctor if you observe any of the following side-effects, especially if they do not go away.