Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some of which are potentially diagnostic of decay, but none of the previous extraction methods have been developed in light of this. To be able to record close to natural deamidation levels of samples, an extraction procedure should minimize laboratory-induced decay, such as asparagine and glutamine deamidations, which are considered most strongly related with decay and known to occur frequently with standard laboratory procedures. Here we tested numerous methods to identify an optimal approach of extracting proteins from bone while minimizing artificial decay. Using a weak acid to partially demineralize the bone sample, then subsequent incubation of the acid insoluble fraction with guanidine hydrochloride and enzymatic digestion in ammonium acetate, we observed an ∼50% reduction in deamidation while also substantially decreasing the protocol length. We propose this optimized method as appropriate for studies of archaeological, palaeontological, as well as potentially forensic investigations using proteomics where decay measurements could act as “molecular timers”.