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Stable isotope analysis of bone and dental collagen is one of the most common methods to investigate the ecology of modern and extinct human and animal populations. However, since bone and dentine are composite materials with both organic and mineral components, the mineral component must be removed prior to analysis. In this study we investigated the timing and efficacy of mineral removal from bone and dentine. We performed a series of time-step experiments that show that mineral removal can be quantified over short periods of time using Fourier Transform Infrared Spectroscopy (FTIR), and collagen alteration can be tracked using a combination of stable isotope analysis and elemental analysis. We tested our methods on three modern materials: mammalian bone, mammalian dentine, and shark dentine. Our results show: 1) mineral removal is a necessary step, as structural carbonate has a strong influence on stable isotope compositions; 2) demineralization using weak acid (0.1M HCL) does not appear to alter the elemental and isotopic compositions of collagen. Our methods can be used as a framework to evaluate the need-for and efficacy of other demineralization methods in use today including EDTA-demineralization and lipid removal.