The mechanism of bonding in biomass pellets is such a complex event to comprehend, as the nature of the bonds formed between combining particles and their relevance to pellet quality are not completely understood. In this study, pure and blended biomass pellets made from Norway spruce and pea starch were characterized using advanced analytical instruments able to provide information beyond what is visible to the human eye, with intent to investigate differences in bonding mechanism relevant to quality. The results, which were comprehensively interpreted from a structural chemistry perspective, indicated that, at a molecular level, the major disparity in bonding mechanism between particles of the pellets and the quality of the pellets, defined in terms of strength and burning efficiency, were determined by variation in the concentration of polar functional groups emanating from the major organic and elemental components of the pellets, as well as the strength of the bonds between atoms of these groups. Microscopic-level analysis, which did not provide any clear morphological features that could be linked to incongruity in quality, showed fracture surfaces of the pellets and patterns of surface roughness, as well as the mode of interconnectivity of particles, which were evidence of the production of pellets with dissimilarities in particle bonding mechanism and visual appearance.