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Butternut squash (Cucurbita moschata) is recognized as a functional food due to its abundant content of health-promoting compounds, including carotenoids and polyphenols. The aim of this study was to examine the impact of industrial freezing stages on the bioaccessibility of carotenoids and polyphenols in organic Butternut squash supplied for baby food. Identification and quantification of bioactive compounds were carried out using UPLC-ESI-MS/MS and HPLC-PDA, respectively. The results revealed that industrial freezing of squash did not cause a significant change in bioaccessibility of α- and β-carotene. On the other hand, frozen squash was found to contain higher levels of bioaccessible epicatechin (main flavonoid) (117.5 mg/kg) and syringic acid (main phenolic acid) (32.0 mg/kg) compared to fresh internal fruit. Moreover, the levels of bioaccessible epicatechin and syringic acid were found to be the highest in discarded pomace and seed sample (454.0 and 132.4 mg/kg, respectively). Overall, this study emphasized that industrial freezing could be an effective strategy for preserving carotenoid bioaccessibility in organic Butternut squash, while also enhancing the levels of bioaccessible polyphenols. In addition, we also demonstrated that pomace and seed, which are discarded as waste, have significant potential to be utilized as a food source rich in bioactive compounds. [ABSTRACT FROM AUTHOR]