This study explores the effect of ultrasound-assisted cellulase (UE) processing on the structure, functional performance, and prebiotic properties of guava insoluble dietary fiber (RIDF). As the ultrasound exposure time increased (0–40 min), the particle size (from 126.3 μm to 38.7 μm) and crystallinity (from 30.72% to 14.42%) of RIDF significantly decreased, while its soluble carbohydrate content (from 1.40% to 6.17%) and water solubility (from 8.6% to 16.4%) notably increased. These crucial changes suggested the degradation and disorganization of RIDF. Meanwhile, UE-RIDF (modified RIDF) demonstrated a honeycomb network microstructure with a larger surface area, indicating distinct structural and morphological properties compared to RIDF. Consequently, UE-RIDF showed stronger retention/adsorption capacity and improved in vitro prebiotic activity. Interestingly, UE treatment increased RIDF fermentability, leading to additional shifts in its modulation of human fecal microbiota, including a higher abundance of Proteobacteria and Phascolarctobacterium. Furthermore, compared to pure cow/goat yogurt, yogurt fermented with UE-RIDF displayed a lower pH, better stability, and improved texture and rheological properties during a 21-day refrigeration period. These findings highlight the potential application of RIDF as a novel prebiotic active ingredient in fermented foods for the first time, underscoring the critical role of UE treatment in enhancing its performance.