Storage Stability of a Multifunctional Fermented Blend Based on Sacha Inchi (Plukenetia volubilis) Oil Press Cake and Yacon (Smallanthus sonchifolius) Flour: Physicochemical Properties, Bioactivity, and Prebiotic–Probiotic Potential

Plant-based symbiotic systems are often limited by poor storage stability and inconsistent biofunctional performance. This study evaluated the stability and functionality of a fermented blend based on sacha inchi (Plukenetia volubilis) oil press cake (SIC) and yacon (Smallanthus sonchifolius) flour (YF) as sources of protein and fructooligosaccharides (FOS), respectively, using two processing strategies: fermentation with Lactobacillus rhamnosus (T1) and combined enzymatic hydrolysis with Alcalase and fermentation with Lactobacillus plantarum (T2). Both treatments maintained viable cell counts (VCC) above probiotic thresholds (>106 CFU mL−1) during 28 days of storage at 4 °C, confirming their suitability as probiotic carriers. Notably, T2 significantly enhanced metabolic activity, as evidenced by higher organic acid production and increased soluble protein content due to Alcalase-mediated hydrolysis, which promoted the generation of bioactive peptides associated with improved antioxidant and antihypertensive activities. Biofunctional properties, including total phenolic content, antioxidant capacity (AC), and angiotensin-converting enzyme (ACE) inhibitory activity, remained stable throughout storage, while FOS degradation was minimal, confirming preservation of prebiotic functionality. LC–MS/MS Q-TOF analysis revealed a complex phenolic profile that was differentially modulated by lactic acid fermentation, with L. plantarum (T2) promoting extensive phenolic biotransformation and increased metabolite diversity, whereas L. rhamnosus (T1) largely preserved the original phenolic profile. These findings demonstrate that the synergistic interaction between enzymatic hydrolysis and L. plantarum fermentation promoted peptide release, intensified microbial metabolism, and enhanced phenolic biotransformation, thereby contributing to the superior functional properties observed in T2, while maintaining stable biofunctional characteristics throughout refrigerated storage in both treatments.