The microbial composition of the food production environment plays an important role in food safety and quality. With the exception of fecal matter, little is known about the microbiota of the egg production environment or the variation in microbial composition and diversity between cage and free-range housing systems. This study employed both 16S rRNA gene sequencing technology and culture-based techniques to investigate the bacterial microbiota of an egg production facility comprising of both free-range and conventional cage housing systems. The study also aimed to detect the presence of Salmonella enterica and determine whether its presence was positively or negatively associated with other taxa. Our findings revealed that microbiota profiles of free-range and cage houses differ considerably in relation to the relative abundance and diversity. Cage samples had significantly higher (p <0.001) alpha diversity measures than free range housing samples. Comparisons of phyla and species-level relative abundances were also highly variable, not only between housing systems, but between different sampling sites within houses with only 36% of taxa present in every sample type. Core to each housing system were known inhabitants of the poultry gastrointestinal tracts, Romboutsia and Turicibacter, as well as common spoilage bacteria. Generally, free-range samples contained fewer taxa and were dominated by Staphylococcus equorum, differentiating them from the cage samples. Salmonella enterica was significantly associated with the presence a bacterium belonging to the Carnobacteriaceae family, Isobaculum melis. The results of this study demonstrate that the diversity and composition of the microbiota was highly variable across the egg layer housing systems, which could have implications for productivity, food safety and spoilage. This study demonstrates that 16S amplicon sequencing can provide a greater understanding of the microbial composition and diversity of samples collected from the food production environment. Such information provides insights into the transmission pathways of microbial populations in egg layer systems which can be used to develop better control strategies.