Microbial fermentation is recognized to improve feed utilization and health of farmed animals. However, its effect on flesh quality and the underlying mechanisms remain understudied. Herein, Bacillus amyloliquefaciens SS1, a probiotic strain isolated from the intestinal tract of Nile tilapia (Oreochromis niloticus) was used to ferment soybean meal (FSM). Two tilapia experimental diets containing FSM and raw soybean meal were formulated for an eight-week feeding trial. Results showed that dietary FSM significantly increased the carcass ratio of fish, while there was no significant difference in weight gain or feed utilization between the two dietary treatments. Texture profile analysis showed that muscle springiness was improved by the FSM diet. There was no discernible difference in myofiber morphology between the two treatments. However, the FSM-fed fish had significantly lower muscle lipid contents than the control, accompanied by suppressed lipogenesis, while lipolysis was promoted both in muscle and liver tissues. Interestingly, the FSM diet modified gut microbial community, resulting in increased propionate concentrations. By establishing a high-fat model using primary hepatocytes of tilapia, we demonstrated the role of propionate in reducing lipid accumulation. Our finding highlights the emerging roles of gut-derived metabolites in affecting flesh quality by modifying host metabolism, providing a foundation for improving the flesh quality of aquaculture fish starting from the feed.