Non-specific lipid transfer proteins (nsLTPs) are small proteins abundant in plants, which function in transferring phospholipids and galactolipids across the membrane. nsLTPs also play a key role in plant resistance to biotic and abiotic stresses, growth and development, as well as in sexual reproduction, seed development, and germination. In addition, these proteins have previously been identified as food allergens. In the present study, we carried out a molecular and functional comparative characterisation of 25 sequences of nsLTPs of lupin legumes and other species. Extensive analysis was carried out; including comparison of databases, phylogeny, physical–chemical properties, functional properties of post-translational modifications, protein structure conservation, 2-D and 3D modelling, functional interaction analysis, and allergenicity including identification of IgE, T-cell, and B-cell binding epitopes. The results indicated that particular structural features of nsLTPs are essential to the functionality of these proteins, high level of structural stability and conservation. Information about different functional interactions between nsLTPs and ligands showed that nsLTPs can accommodate several of them with different structure; and that the relationship between structure and allergenicity was investigated through the identification of epitopes susceptible of being involved in cross-reactivity between species of the Fabaceae family.