Ewe’s milk cheese produced from raw milk holds cultural and economic importance in Southern European countries; however, it poses microbiological challenges. Among spoilage microorganisms, Pseudomonas fluorescens is particularly concerning due to thermostable enzymes that impair the texture, aroma, and stability of cheese, even under refrigeration and salinity. This study evaluated the influence of sodium chloride concentration on Pseudomonas fluorescens given the pivotal role of salt in ensuring cheese stability and safety. Cheeses inoculated with Pseudomonas fluorescens were produced under an experimental design that combined three ripening temperatures with four salt concentrations. Physicochemical composition and microbiological stability were assessed at the end of ripening (20 days). Results showed that the ripening temperature emerged as the most determinant factor, influencing microbial viability and increasing solid retention, proteolysis, and dehydration, leading to harder cheeses. Low temperatures without salt favoured surface colour defects, whereas, although high salt levels contributed to partial control of Pseudomonas spp., they also delayed ripening, resulting in cheeses with a pale, uncharacteristic appearance. Conversely, moderate salinity (2%) combined with higher ripening temperatures promoted uniform maturation, resulting in a stable texture and appearance free of defects. These findings highlight the need to balance salt and ripening conditions to optimise quality and safety in traditional raw ewe’s milk cheeses.