Meat discoloration, lipid oxidation, and undesirable texture are inevitable phenomena in basa fish fillets during storage, which in turn limits their exportation as well as decreases consumer acceptability. In addition, increasing consumers’ requirements for high-quality, minimally processed, and ready-to-cook fish fillets with an extended shelf-life is a great challenge, particularly with lifestyle changes. Accordingly, this study aimed to improve the quality, lipid stability, fatty acid profile, and lipid nutritional quality indices (LNQI) of basa fish fillets during chilling storage at 4 °C for 15 days using pepsin enzyme (E, 0.1%), rosemary oil (R, 0.5%), citric acid (CA, 0.5%), and their combination (0.1% E + 0.5% R; 0.1% E + 0.5% CA; and 0.1% E + 0.5% R + 0.5% CA). Our results revealed that all treated samples exhibited a significant increase in protein content, a significant decrease in fat content, and a marked reduction in pH, total volatile base nitrogen (TVBN), thiobarbituric acid (TBA), free fatty acids, and shear force (SF) values in comparison to control ones. Moreover, significant improvements in sensory scores, color stability, fatty acid profile, LNQI, and microbial quality of all treated samples were observed. Such findings were more pronounced in samples treated with a mixture of pepsin, rosemary, and citric acid (TVBN: 2.04 vs. 6.52 mg%; TBA: 0.40 vs. 2.68 mg malonaldehyde/Kg; and SF: 8.58 vs. 19.51 Kgf). Based on the obtained results, there was an extension for the shelf life of all treated basa fish fillet samples, especially in samples treated with a mixture of pepsin, rosemary, and citric acids when compared with the control samples (˃15 days versus 10 days). Additionally, eucalyptol, camphor, isoborneol, and α-pinene are the main components of rosemary, with great antioxidant and antimicrobial activity. In conclusion, the mixture of pepsin, rosemary, and citric acid can be applied easily in the seafood industry and at the household level to provide ready-to-cook fish fillets of high quality with great health benefits.