Although Brazil is currently the world’s eighth largest egg exporter, the shift of consumers towards free-range eggs may present new sanitary challenges. This study aims to evaluate the microbiological vulnerability of eggs and environmental conditions in a farm certified for both conventional and free-range systems using two standard methods (enterobacteria counting and Salmonella spp. survey). Two high-producing farms were selected for this study, one under both conventional and free-range systems at the same place as the test farm, and another under conventional system only as a control farm. Enterobacteriaceae counts were determined for eggshells; and detection of Salmonella spp. was conducted in eggs, nest box material, feeder, and sponge samples from water dispensers, feeders, production plant, besides water samples from nipple dispensers and artesian well. The average enterobacteria count (log CFUmL-1) was 0.09 for conventional and 1.73 for free-range systems (p < 0.001). While Salmonella spp. was not detected in the conventional system but was present in one feeder and three eggshells from the free-range system. Therefore, the conventional system demonstrated better hygiene-sanitary status than the free-range one. Moreover, controlling food safety should always be considered when improving animal welfare.