Faba bean (Vicia faba L.), also known as broad bean, has recently experienced renewed interest due to its potential as a functional food, in conjunction with its rising use in plant-based meat alternatives. Australia is the fourth largest producer of faba bean and is the largest exporter, being responsible for one-third of the international trade market. In this study, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy was applied to ten commercial varieties of Australian faba bean, in order to profile the differences in the sub-molecular structural composition of the major nutritional constituents, namely proteins, starch, structural carbohydrates and lipids. Following identification of the major structural features present and their various secondary structures, quantification of the peak heights and areas allowed differences in the relative proportion of various structural carbohydrate and amide constituents to be observed between varieties. Key varietal differences were observed in the ratios of α-helices: β-sheet protein structures (range 0.945 – 0.956) and crystalline: amorphous starch structures (range 0.884 – 0.904). Given that the secondary structure of nutritive compounds influences their digestibility in vivo, these differences in secondary structure may contribute to the differential digestibility or nutritional value of seed material from these varieties. ATR-FTIR shows promise for the rapid assessment of such structural features in intact crops.