This work involves the application of physical separation methods to concentrate the pigment of semi-defatted annatto seeds, a noble vegetal biomass rich in bixin pigments. Semi-defatted annatto seeds are the residue produced after the extraction of the lipid fraction from annatto seeds using supercritical fluid extraction (SFE). Semi-defatted annatto seeds are use in this work due to three important reasons: i) previous lipid extraction is necessary to recovery the tocotrienol-rich oil present in the annatto seeds, ii) an initial removal of the oil via SFE process favors bixin separation and iii) the cost of raw material is null. Physical methods including i) the mechanical fractionation method and ii) an integrated process of mechanical fractionation method and low-pressure solvent extraction (LPSE) were studied. The integrated process was proposed for processing two different semi-defatted annatto materials denoted Batches 1 and 2. The cost of manufacture (COM) was calculated for two different production scales (5 and 50 L) considering the integrated process vs. only the mechanical fractionation method. The integrated process showed a significantly higher COM than mechanical fractionation method. This work suggests that mechanical fractionation method is an adequate and low-cost process to obtain a rich-pigment product from semi-defatted annatto seeds.