The present work proposed a two-step sequential scCO2 extraction process to selectively extract the main bioactive compounds from annatto seeds, geranylgeraniol and tocols, aiming to diversify and to improve the added-value of annatto seeds products. Firstly, pressure (10, 17, 24 and 31 MPa) and temperature (40 and 60 °C) conditions resulting CO2 densities ranging from 290 kg/m3 to 915 kg/m3 were investigated to verify its effect on the chemical composition of the extracts. Extracts obtained at 290 kg/m3 presented the highest geranylgeraniol content (39 ± 9%) and the lowest tocotrienols content (0.95 ± 0.04%). CO2 densities higher than 629 kg/m3 were needed to recover tocotrienols-rich fractions. Therefore, a two-step sequential scCO2 extraction process was carried out using 60 °C and 10 MPa (290 kg/m3) in the first step to recover the geranylgeraniol-rich fraction, and 40 °C and 20 MPa (840 kg/m3) in the second step to recover the tocotrienols-rich fraction.