The effect of cooking (C) unripe banana fruits at different times (5, 15 and 25 min), followed by annealing (ANN) and annealing + storage (ANN+S) were evaluated. Cooking of unripe banana fruit for longer times (15 and 25 min) decreases the RS content, but increases the SDS fraction. Granular aggregates were produced, which could be formed by partially gelatinized granules. ANN and ANN+S increased the RS content, while the SDS value did not change. The pasting behaviour of ANN and ANN+S showed low viscosity without breakdown or setback due to the restricted amylose leaching, which was higher in flours with ANN+S. The ANN and ANN+S increased the gelatinization temperatures while the annealed and stored samples showed an increase in the crystallinity level due to reorganization of the granular structure compared with native and cooking treated samples. It is possible to combine different treatments to modify the starch digestibility of unripe banana flour, due to that changes in the granular conformation were produced, which decrease its ability to swell and to gelatinize.