Tropical environments in the Indo-Pacific pose a challenge for bone preservation. In addition to fragmentation, multiple accumulator agents in caves, and post-depositional processes, the deterioration of organic matter comprises a further constraint for zooarchaeology. In recent years, palaeoproteomics (i.e., the analysis of ancient protein) have provided promising results for taxonomic identification of bone fragments lacking diagnostic markers. Nevertheless, these studies have focused on assemblages from temperate environments, while the potential of palaeoproteomics in tropical settings still remains mostly unexplored. In these settings, palaeoproteomics can allow researchers to distinguish between domesticates and wild specimens, to differentiate between closely related families, and to discuss past biogeographic distributions of species. However, poor preservation of collagen in these environments has impacted on the development of reliable screening methods for testing bone collagen preservation, which is crucial to evaluate the feasibility of palaeoproteomics in an archaeological assemblage. We present a new cost-effective method to test collagen preservation before attempting palaeoproteomic analyses. By combining results from bone nitrogen content analysis, FTIR, and protein assays, we propose a baseline to evaluate collagen preservation in Indo-Pacific sites. We apply our methods on a modern assemblage of pig bones buried in guano deposits for a maximum of 24 months. The experimental results were later applied to archaeological bones from Widgingarri 1 (Kimberley, Australia), to assess the feasibility of palaeoproteomics to identify bone fragments in this site. Our results demonstrate how pre-screening of bones through these techniques will save time and money prior to time-consuming palaeoproteomic analysis, as well as minimizing bone destructive analyses on samples which low collagen content makes them unsuitable for radiocarbon dating and palaeoproteomic analyses.