Intake of high quantities of dietary proteins sourced from dairy, meat or plants can affect body weight and metabolic health in humans. To improve our understanding of how this may be achieved, we reviewed the data related to the availability of nutrients and metabolites in the faeces, circulation and urine. All protein sources (≥20% by energy) increased faecal levels of branched chain fatty acids and ammonia, and decreased the levels of butyrate. There were metabolites responding to dairy and meat proteins (branch chain amino acids) as well as dairy and plant proteins (p-cresol), which were increased in faecal matter. Specific to dairy protein intake, the faecal levels of acetate, indole and phenol were increased, whereas plant protein intake specifically increased the levels of kynurenine and tyramine. Meat protein intake increased the faecal levels of methionine, cysteine and alanine, and decreased the levels of propionate and acetate. The metabolite profile in the faecal matter following dairy protein intake mirrored availability in circulation or urine. These findings provide an understanding of the contrasting gut versus systemic effects of different dietary proteins, which we know to show different physiological effects. In this regard, we provide directions to determining the mechanisms for the effects of different dietary proteins.