Faunal remains play an important role in helping reconstruct Palaeolithic hunter-gatherer subsistence and mobility strategies. However, differential bone preservation is an issue in southern European prehistoric sites, which often makes morphological identification impossible. Zooarchaeology by Mass Spectrometry (ZooMS) is a new, low-cost method that can improve NISP statistical significance in a replicable way by using diagnostic peptides of the dominant collagen protein as a fingerprint of animal (including hominin) species. It is also a powerful tool to assess collagen preservation for radiocarbon dating. This paper presents the proof of concept of a method for evaluating collagen preservation in a quick and minimally destructive way in the field prior to ZooMS analysis by using a portable Fourier Transform Infrared Spectrometer (FTIR) equipped with an attenuated total reflectance accessory (ATR). The method was tested on faunal assemblages from two north-western Italian sites: Riparo Bombrini and Arma Veirana. Both are important sites for understanding the Middle and Upper Palaeolithic of Liguria but are located in two distinct environmental contexts (coast vs. mountainous hinterland) that impacted collagen preservation. The relative abundance of collagen in powdered bone samples was evaluated by calculating the Amide I to phosphate ratio (CO/P) from spectra collected with two portable and three laboratory-based FTIR instruments. The bones were then analysed by ZooMS and the results were compared to evaluate the effectiveness of using FTIR as a screening technique. Results indicate that FTIR instruments are excellent tools to predict collagen preservation in fragmented archaeological bones, but a screening method should be first calibrated on the analysed faunal assemblage by conducting a test of the CO/P screening procedure with various measurement systems on a single FTIR instrument.