L-Cysteine (L-Cys) pre-treatment at two concentrations (150 mg/kg; PC1 and 300 mg/kg; PC2) on potato starch was conducted to produce starch-cysteine conjugates. Afterward, the effect of α-amylase on starch digestibility of potato native (PE) and starch-cysteine conjugates (PC1E and PC2E) were examined. Thiolation not only damaged starch according to the formation of pore and blister-like spots on the surface of starch granules, but also provided the functional group to immobilize α-amylase. Starch-cysteine conjugates showed a significantly greater degree of hydrolysis 24.1 % (PC1E) and 36.5 % (PC2E) in comparison with (16.8 %; PE). Destroying the granules integrity were accompanied with decreased crystallinity from 37.7 % to 33.1 % (PC1), 31.1 % (PC2), 27.6 % (PC1E) and 22.4 % (PC2E) with increasing thiol content (%) on surface from 2.3 %; PC1 to 3.4 %; PC2. The ratio of 1047/1022 cm− 1 reduced from 1.112 (native potato starch) to 0.974 (PC1E) and 0.867 (PC2E) after being subjected to α-amylase. Additionally, substantially low pasting viscosities (determined by RVA) along with the thermal properties (determined by DSC) of starch-cysteine conjugates treated with α-amylase could confirm the degradation of molecular structures containing low swelling power.