This study demonstrated the selective support of pomelo (Citrus maxima) peel extract (PPE) on Lactiplantibacillus plantarum 299 V growth, of which the resultant enhanced microbial safety and shelf life of salmon fillets. Incorporating PPE fermented with L. plantarum 299 V for 48 h (FPPE-48h) into alginate coating inhibited both the spiked Listeria monocytogenes and the spoilage - causing bacteria (psychotrophic bacteria, Enterobacteriaceae, Pseudomonas spp.) on salmon fillets during the 4-day chilled storage, resulting in 1–1.5 log CFU/g lower bacterial counts (P < 0.05). FPPE-48h effectively suppressed biogenic amine-producing bacteria, and remarkably retarded the accumulation of putrescine, cadaverine, histamine, and tyramine (P < 0.05). Last, the key antimicrobial substances generated during the late stage of PPE fermentation were profiled using non-target ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) analysis. This study exemplifies a successful approach of fermenting probiotic utilizing food by-products/food waste to enhance the safety and shelf life of ready-to-eat foods.