The microbiological quality of goat milk needs to be monitored to ensure the milk and milk products are safe for consumers. Our previous studies have demonstrated high contamination of goat milk by coagulase-positive and coagulase-negative Staphylococcus spp. that frequently harbor enterotoxin-producing genes. Staphylococci have been associated with food-poisoning outbreaks in humans and because staphylococci are commonly isolated from goat milk and are have an important effect on public health, these organisms are used as indicators of contamination in goat dairy plants. Therefore, this study aimed to evaluate the epidemiology of Staphylococcus spp. at different points of small-scale processing plants of goat milk in northeastern Brazil, the leading goat milk-producing region in the country. A longitudinal study was performed in 2 goat milk processing plants; samples of raw and pasteurized milk and swabs of the inner surface of equipment, walls, and handlers’ hands were collected. Samples were collected in the morning before milk processing to detect residual contamination. Staphylococcus spp. isolates (n = 36) were subjected to genotyping by REP-PCR using the primer RW3A. Indistinguishable genotypic profiles were observed among Staphylococcus spp. collected from milk samples, equipment, and handlers’ hands, indicating the presence of residual contamination during milk processing and the need to improve cleaning and disinfection procedures. The Staphylococcus spp. isolates from handlers’ hand swabs had high genotypic relatedness with isolates from equipment and pasteurized milk, indicating that workers can play a role in the cross-contamination by Staphylococcus spp. in milk processing plants.