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Annona cherimola Mill. seeds are a residue of the industrial processing of this fruit, for which, presently, there is no industrial application. They have a considerable amount of oil, which can be converted into biodiesel, but the remaining lignocellulosic fraction still needs relevant added-value valorization routes. In this work, the selective hemicelluloses removal by autohydrolysis was optimized aiming to maximize the yield of oligosaccharides with potential applications in food, pharmaceutical and cosmetic industries. A maximum of 10.4 g L−1 of oligosaccharides was obtained, for a severity factor of 3.6, where 74.5% of the original hemicellulose was solubilized. The process kinetics is presented, modeled (based on the Arrhenius equation) and its scale-up is discussed. The hydrolyzate shelf-life was evaluated and the produced oligosaccharides are stable at room temperature for, at least, 3 weeks. Furthermore, all oligosaccharides are also stable at 100 °C for 1 h, in pH values between 1 and 11, enabling their industrial processing, and at 37 °C for 3 h, in pH values between 1 and 3, thus indicating its potential classification as non-digestible oligosaccharides. The remaining cellulose enriched solids presented an increased enzymatic digestibility (as a function of the autohydrolysis severity) that assures its efficient use in subsequent processes (e.g., bioethanol production). The upgrade route developed in this work in combination to the previously reported use of A. cherimola seed oil for biodiesel production can lead to an integrated zero-waste valorization strategy within the biorefinery framework.