The interest in natural colorants derived from sustainable processes has prompted research into obtaining bixin from defatted annatto (Bixa orellana L.) seeds. Bixin is a compound that imparts yellow-orange-red coloration, known for its high biodegradability, low toxicity, and wide industrial applicability. Meanwhile, high-intensity ultrasound (HIUS) technology has emerged as a promising method for extracting natural colorants, offering higher yields through shorter processes and minimizing thermal degradation. Although some studies have demonstrated the efficiency of HIUS technology in bixin extraction, research on the effects of acoustic cavitation on the properties of the colorant remains limited. Therefore, this study aimed to investigate the influence of HIUS-specific energy levels (0.02, 0.04, 0.12, and 0.20 kJ/g) on the chemical, physical, and morphological characteristics of annatto extracts containing bixin and geranylgeraniol. Single-step extractions of bixin using ethanol as a solvent were evaluated at various acoustic powers (4.6, 8.5, 14.5, and 20 W) and extraction times (0.5, 1, 3, and 5 min) to determine their impact on the yield of natural colorant extraction. Increasing the acoustic power from 4.6 to 20 W and extending the extraction time from 0.5 to 5 min resulted in higher yields of natural colorant, likely due to the effects of acoustic cavitation and increased heat under more intense conditions. However, elevated levels of mechanical and thermal energy did not affect the chemical properties of the colorant, as indicated by UV–Vis and FTIR spectra. Conversely, higher specific energies yielded colorants with a more intense red hue, consistent with increased bixin content, and altered the microstructure and physical state, as observed in X-ray diffractograms. Nevertheless, these alterations did not impact the solubility of the colorant. Therefore, employing a cleaner extraction procedure aided by one-step ultrasound facilitated the recovery of natural colorants and contributed to the biorefining of annatto seeds, enabling the production of a rich geranylgeraniol colorant through a sustainable approach.
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