The presence of original organic matter and retention of an indigenous isotopic signal in fossils have been disputed for years. An experiment was conducted to evaluate the influence of diagenesis on bone-protein isotope values, analyses were conducted on Holocene and Pleistocene fossils from Natural Trap Cave (NTC), Wyoming. Modern cow, Bos taurus, bone was heated with and without excess water for up to 195 hours at 100°C in an inert atmosphere. Collagen and non-collagenous proteins (NCP) were extracted and analyzed isotopically. Under dry conditions, carbon and nitrogen isotope values change by less than 0.4‰ during the 0 to 195 hour interval. In the presence of excess water, carbon and nitrogen isotope values change by no more than 1.0‰ and 0.5‰, respectively, over 192 hours. The relative abundance of amino acids of collagen from heated bone differs by less than 10% from that of unheated collagen. Protein preservation is indicated by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) that strongly indicates a portion of the original osteocalcin exists intact in samples heated for 195 hours. Good preservation of collagen in NTC fossils is implied by high collagen yields, C:N, and realistic trophic structures based on isotope values. Carbon and nitrogen isotope values of ancient collagen increase with trophic level, allow dietary assessments to be made, and differentiate between ruminant and non-ruminants. The results indicate that isotope values are resilient during simulated diagenesis and suggest that an indigenous isotopic signal can exist in well-preserved fossils such as those from NTC.