Recently, legumes starch were studied extensively due to high amylose and resistant starch contents, and low glycemic index (GI). We evaluated the impact of autoclaving-cooling cycles (single, triple, five) on the physicochemical properties, in vitro starch digestibility, and estimated glycemic index (eGI) of cowpea starch. Autoclaving-cooling increased the amylose content, water/oil holding capacities, onset, peak, and conclusion gelatinization temperatures. Pasting temperature, gelatinization enthalpy, final and setback viscosities significantly decreased (P < 0.05) in modified cowpea starches. RS content increased from 32.14 ± 1.33% to 41.26 ± 0.81%. Autoclaving-cooling altered the crystalline structure of cowpea starch from C-type to a mixture of the B and V-types. FT-IR spectra indicated an increase in the ratio of 1049 cm-1/1018 cm-1 and 995 cm-1/1018 cm-1 which suggested an increase of the amount of crystallite and double helix in modified starch. The eGI decreased from 47.94 ± 0.45 to 41.46 ± 0.06 and was categorized as a low GI food. These results suggested that single autoclaving-cooling cycle could be a possible method to produce resistant starch from cowpea starch with better thermal stability and lower GI. Both native and modified cowpea starch were categorized as high RS and could be used as an alternative source of resistant starch from legume starch for developing functional foods.