Physico-chemical, retrogradation, rheological properties and in vitro digestibility of lysine incorporated kithul starch modified by annealing, heat moisture treatment and its combinations were studied. LS-AHMT (annealed-heat moisture treated lysine incorporated kithul starch) exhibited lowest amylose leaching. LS-AHMT showed significantly (P ≤ 0.05) higher relative crystallinity. LS-ANS (annealed lysine incorporated kithul starch), LS-HMT (heat moisture treated lysine incorporated kithul starch) and LS-AHMT formed more weak gel by the effect of annealing, heat moisture treatment and its combination. LS-AHMT showed lowest pasting viscosities, G 0 and G″ values among the modified kithul starch, which indicates its lower retrogradation properties. In vitro digestibility of kithul starch decreased after modifications and LS-ANS, LS-HMT and LS-AHMT showed significantly higher resistant starch content. The current study showed that annealing, heat moisture treatment and its combination on NS-LS (lysine incorporated kithul starch) effectively modified kithul starch properties.