Many studies have shown that carcass contamination at slaughter is strongly correlated with the microbiological profile of the animal’s hide rather than its faeces. Metagenomic/phylogenetic analysis provides an opportunity to further describe the relationship between hide, faecal and carcass samples. For this investigation, samples were taken from matched hides, carcasses, and faeces from every fifth animal for a total of 50 animals during a single processing day. RNA was extracted and 16s RNA amplicon analysis was performed to determine the type and abundance of microbes present. Source tracking analysis demonstrated that 60% of bacteria on the carcasses are most likely derived from the hide and the remainder from other environmental sources. Microbes on carcasses were of low abundance and complexity with the two most abundant taxa being Pseudomonas and Staphylococcus epidermidis. Interestingly, neither of these taxa were detected on the hide or in faecal samples. Approximately 1% of the microflora on the carcass were Anoxybacillus kestanbolensis, a thermophile more frequently associated with geothermal springs than meat processing environments. Faecal contamination of hides was low and the source of this contamination was not necessarily the same animal. Highly contaminated hides did not appear to contaminate the resultant carcass but most likely contributed to a generalized contamination in the processing environment. Microflora present on the hide were primarily aerobes with many taxa derived from the Moraxellaceae. Faecal microflora had a typically high level of diversity as has been observed previously and was dominated by firmicutes and bacteroidetes. A single faecal sample varied from the typical composition with higher than normal levels of Escherichia (approximately 33% of all reads for this sample). This work provides a novel view of microbial ecology in the abattoir and suggests that management of aerosols and particulates derived from the hide is extremely important to meat hygiene.