Coalho cheese is a typical Northeastern Brazilian food whose production and consumption has expanded considerably to other regions of the country. Despite its cultural and socioeconomic relevance, coalho cheese still has a negative reputation due to problems in its physicochemical and microbiological quality standards, especially when it is produced artisanally. For this reason, many researchers have been looking for alternatives to improve the quality and the notoriety of this product, such as the application of probiotic strains to inhibit pathogens. However, in addition to the research related to the desired probiotic properties and the safety of strains for food application, it is important to know the possible changes in the food matrix caused by this intervention. In this context, the aim of this study was to evaluate the effect of the incorporation of probiotic strains of Enterococcus faecium on the physicochemical and sensory characteristics of coalho cheese. The cheeses were made with pasteurized cow milk and probiotic strains of E. faecium were added during production. Cheeses were also made without adding the strains, and considered as control cheeses. The final products were evaluated for moisture, pH, titratable acidity, total carbohydrates, proteins, lipids, ash, color, organic acid profile, and sensory attributes. In addition, viable lactic acid bacteria were also assessed. Coalho cheeses containing E. faecium showed higher titratable acidity and lower pH. In addition, there was a reduction in the carbohydrate content, which was attributed to lactose degradation. The organic acid profile also varied, as highlighted by the increase in the concentration of lactic acid by a factor of 3.5, and by the absence of citric acid as a possible result of the metabolism of E. faecium in the production of aromatic compounds. There was no variation in the color or sensory acceptance of the cheeses. Therefore, the application of probiotic strains of E. faecium in coalho cheese production changes some physicochemical characteristics while maintaining essential properties, such as the color and sensory acceptability of the final product.