Hydrothermal modification treatment (HMT) using hot pressurized water assisted by supercritical CO2 (sc-CO2) over polymers present in semi-defatted annatto seeds (DAS) was performed. DAS was milling and fractionated according to particle size in fine particles (FP) and annatto seed flour (ASF). The raw material for HMT was specifically the ASF fraction. HMT was performed at 80 °C, using a total solvent flow rate of 3 mL/min during 30 min, and the independent variables pressure (150, 200, 250, 300 and 350 bar) and water/sc-CO2 ratio (20/80, 30/70 and 40/60). HMT caused simultaneously a physical modification and a hydrolysis reaction in annatto polymers. The physical modification of polymers (mainly starch) produced in the ASF −remained in the reaction bed- a decrease in the pasting temperature, peak and final viscosity. The hydrolyzed products indicate that the best results for monomers and oligomers of sugar were a water/sc-CO2 ratio of 40/60 and 350 bar.