This study explores a systematic multistep extraction process to valorize various fruit seeds (mango, cherry, lemon, pumpkin, avocado, litchi, peach, and apricot) by fractionating and isolating different fiber components. A first mild treatment, i.e., a protease-assisted extraction, was employed to disaggregate the plant cell structure and isolate soluble fibers. Subsequently, the insoluble residue underwent extraction by hot acidic water to solubilize and separate the pectin fraction. The remaining solid material was finally subjected to hydrothermal treatment to recover recalcitrant hemicellulose. Cherry, lemon, and pumpkin seeds emerged as the most advantageous by-products overall, showing great extractable quantities of low molecular weight pectin, pectin oligosaccharides, arabinogalactans, xylan, and xylo-oligosaccharides (extraction yields up to 63% and 68% in the first and third step, respectively). Peach and apricot seeds yielded fiber extracts that were similar to each other but distinct for each fraction, suggesting potential applications in different food formulations, albeit with lower yields. The purity of the extracts increased with each stage, reaching 42.6% for soluble fibers, 67.3% for pectin, and 76.1% for hemicellulose. Mango, avocado, and litchi seeds were less suitable for this method but could be utilized for starch recovery. This cascade process effectively maximizes the utilization of fruit by-products, offering a scalable solution for the sustainable extraction of valuable fibers.