PurposeThe objective of this study was to evaluate the technical-economic process efficiency of obtaining simultaneous lipo-soluble (LSF) and water-soluble (WSF) fractions from annatto seeds.Design/methodology/approachThe batches of annatto seeds were submitted to the refrigerated solid-liquid extraction process in four stages: pre-extraction, aqueous extraction, separation by decantation and filtration. After that, LSF and WSF from annatto seeds were obtained. The process efficiency and the quality of LSF and WSF were analyzed in terms of average yield and bioactive compounds (bixin, norbixin, phenolics and flavonoids) and their antioxidant and antimicrobial activities. Furthermore, they were economically evaluated in terms of costs of manufacturing and profitability parameters.FindingsThe process was efficient in terms of overall average yield (LSF = 8.68% and WSF = 2.76%) (w/w) and in terms of quality, mainly with higher average yields of bixin (82.34% in LSF) and norbixin (29.59% in WSF) (w/w). The concentration of bioactive compounds in the fractions promoted an increase in inhibiting free radicals (DPPH* and ABTS*+) and in the ferric-reducing power (FRAP). LSF showed a minimum inhibitory concentration of 0.06 mg mL-1 for S. aureus and 0.13 mg mL-1 for S. Typhimurium and S. Enteritidis. The lowest manufacturing costs were obtained for the LSF due to its higher extraction yield compared to the WSF. Plants on an industrial scale of 100 and 1000 L were considered economically viable, with a return on investment of 5 and 2 years.Originality/valueThus, fractions (WSF and LSF) can be applied as natural additives, as sources of bioactive compounds for nutraceutical and/or pharmaceutical, and in the development of other innovative processes. These results have practical applicability for pharmaceutical and food industry.Highlights Green processing of annatto seeds obtains fractions rich in antioxidant compounds.Efficiently presents a high yield of bixin and other bioactive compounds.Effective in concentrating compounds that inhibit microbial growth.Fractions are more accessible sources of bioactive compounds for isolation.Cost of manufacturing (COM) and profitability are studied.