Milling performance is an important attribute for desi chickpea and other pulses, as varieties that are more difficult-to-mill lead to processing yield loss and damage to the resulting split cotyledons (dhal) such as chipping and abrasion which are unattractive to the consumer. Poor milling performance leads to poor dhal quality and therefore lower prices and profitability along the pulse value chain. The Pulse Breeding Australia Chickpea Program identified near-isogenic desi lines that differed in seed shape and milling yields, however it was unknown whether this was due simply to a difference in physical forces on the seed during milling, mediated by seed shape, or whether there were underlying differences in chemical composition that could explain these differences. The two isolines differed in the composition of their seed coat, cotyledons and adjoining surfaces. Some of these differences were in agreement with previous research on composition of easy- and difficult-to-mill samples. These differences suggest that biochemical adhesive or cohesive mechanisms at the interface of seed tissues involve pectic polysaccharides and lignin-mediated binding.