Due to its low tolerance to external factors such as enzymes, dentin collagen often requires stabilization, which can be achieved through cross-linking. In this study, qualitative and quantitative Fourier transform infrared (FTIR) analyses were used to assess dentin collagen stabilization effects of three structurally-different flavonoids -A-type linkage proanthocyanidins (A-PA), B-type linkage proanthocyanidins (B-PA), and epigallocatechin gallate (EGCG), all from natural extracts. Particularly, transmission FTIR spectroscopy was used for the first time to quantitatively assess the biodegradation of fresh ultra-thin (10 µm) dentin collagen films caused by collagenase digestion. Two traditional analytical methods, namely the hydroxyproline assay and weight loss analysis, were also used for comparison purposes. The results from all three methods showed consistently that A-PA and B-PA provide better collagen stabilization than EGCG at concentrations of 0.65% and 1.3% (p<0.01). FTIR is demonstrated to be a valuable and reliable analytical tool for qualitative and quantitative evaluation of ultra-thin collagen films.