Salmonella enterica is among the most important foodborne pathogens. In Ecuador, there is limited information about non-typhoidal S. enterica occurrence in raw meats, its serotype distribution, and antimicrobial resistance. In this study, we addressed this issue in 1095 retail fresh meats (chicken, pork, veal, lamb, beef, and turkey) in Quito by performing a traditional culture methodology and molecular detection. We found that S. enterica was present in 38.1% of the samples, and Salmonella Infantis was the most common serotype showing a high antibiotic resistance and a wide host range. Some host-adapted serotypes were found in uncommon sources of meat, suggesting cross-contamination and the need to implement good manufacturing practices in meat processing. High levels of multidrug resistance were found in all serotypes. There is an urgent need to identify Salmonella serotypes in food to compare with clinical data and to carry out epidemiological studies to control and prevent outbreaks and infections.