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SUMMARY: This study aims to characterize the environmental microbiota of an egg-producing farm situated in Rio Grande do Sul, Southern Brazil, spanning from the chick to the laying hen stages and encompassing the treatment of carcasses and manure. Metataxonomy analyses reveal the continuity of bacterial diversity across the production stages (chick, pullet, and laying hen). The presence of Fusobacteriota and Cyanobacteria in poultry environments before any manure or carcass treatments (named pre-treatment samples) are identified as indicative phyla markers for healthy animals. Nonetheless, alterations in the bacterial communities emerge during the treatment of manure and carcasses (treatment samples), revealing an increased abundance of Halanaerobiaeota. In summary, the study underscores the key phyla influencing the entire environment of the egg production process on a farm in South Brazil. Although our data is from a specific farm, it provides insights for a more robust and representative study of the egg chain.