Sodium chloride reduction in foods is a significant focus of the dairy industry; however, it can interfere with dairy product quality. Thus, researchers have carried out studies on alternatives to maintain dairy product safety when presenting reduced NaCl content, such as natural antimicrobial addition. Caryocar brasiliense (pequi) is a fruit with high phenolic compound concentrations in the pulp and peel and known antioxidant and antimicrobial properties. This study aimed to define the optimum stage for pequi waste extract addition during cheese manufacturing in order to maintain and prolong the shelf life of reduced-sodium goat Minas Frescal cheese.Four different goat Minas Frescal cheese treatments were carried out: control cheese (without extract; CC), pequi extract addition to milk (CM), pequi extract addition to mass (CS), and cheese immersion in pequi extract (CIE). The treatments were subjected to microbiological (Staphylococcus spp., Escherichia coli, Enterobacteriaceae, coliforms and fecal coliforms, Lactococcus spp., and lactic acid bacteria counts), textural (hardness and consistency), and instrumental color (luminosity, yellow intensity, red intensity, chroma, hue angle, and total color change) analyses. No Enterobacteriaceae, Staphylococcus spp., E. coli, or coliforms and fecal coliforms were detected during storage for any of the assessed samples, including CC. Regarding texture, all samples presented a trend for decreasing rigidity during storage. In addition, lower luminosity values were also observed in cheeses produced with added pequi extract (CM, CS, and CIE) when compared with CC. All cheeses produced with added pequi were stable regarding all evaluated parameters; however, pequi extract addition to milk (CM) was shown to be more efficient, leading to higher textural parameters and better microbiological quality during storage. Thus, the CM treatment is the most recommended for pequi waste extract addition during Minas Frescal cheese manufacture.