Fruit residues generated across the global food supply chain constitute a rapidly growing, biologically reactive waste stream that, when left unmanaged, degrades environmental and agricultural quality, whereas controlled microbial fermentation offers a practical means of transforming this waste into stabilized, biologically active soil amendments. This review synthesizes evidence from field trials, greenhouse experiments, and microbiome studies published between 2009 and 2025 to evaluate the agronomic and microbiome-level effects of fermented fruit waste (FFW) as a soil amendment within circular waste-management frameworks. FFW application has been associated with increases in soil organic carbon of 12–24%, microbial biomass carbon of 38–64%, and plant biomass accumulation of 15–35% relative to unamended controls, with the magnitude of these effects varying substantially across studies according to feedstock composition, soil type, crop species, and fermentation method, rather than reflecting a single generalisable effect size. At the rhizosphere level, fermentation-derived substrates selectively recruit plant-growth-promoting rhizobacteria and phosphorus-solubilizing taxa, enhancing nutrient-use efficiency and microbial network resilience. These findings indicate that FFW functions not merely as a recycled nutrient input but as a biologically transformed amendment that actively restructures soil microbial communities and reinforces plant–soil feedback networks, while practical constraints such as phytotoxicity, salinity accumulation, pathogen survival, and feedstock contamination require evidence-based mitigation. However, standardized fermentation protocols, quantitative process-parameter thresholds, and long-term field validation remain limited, underscoring the need for future research integrating process optimization with multi-site field trials to enable reliable, microbiome-guided FFW application at scale.