Background: Rural communities who consume unpasteurized and traditional fermented milk products on a regular basis, have a low prevalence of allergic diseases. Lactic acid producing bacteria present within these products, is postulated to have an allergy protective role against atopy. Objective: To characterize and compare the bacterial microbiota of fresh unpasteurised cow’s milk and to explore the effect of milk fermentation (commercially and traditionally fermented) on the bovine milk microbiota. Methods: Raw, unpasteurized cow’s milk was collected from urban and rural farms. Another sample, collected from a rural farm, was left to ferment naturally. Three different brands of commercially fermented milk samples were also analysed. The V3 and V4 regions of the 16S rRNA gene were amplified to assess microbiota composition. Results: Urban and rural fresh milk had the highest microbiota alpha diversity, and commercially bought fermented milk products, the least. Commercially fermented milk was consistently dominated by lactic acid producing bacteria, belonging to the phylum Firmicutes, while homemade fermented milk comprised of approximately 50% Firmicutes and 50% Proteobacteria. The relative abundance of several organisms differed between fermented and unfermented milk. Lactococcus lactis dominated all milk products, however its relative abundance was lower in fresh milk compared with fermented milk. Lactobacillus paracasei and Streptococcus infantis were abundant in traditionally fermented milk, but absent in commercially fermented products. Potential pathogens were demonstrated in fresh and home fermented milk. Conclusion: Commercially fermented milk can be promoted as a safe and possible allergy protective complementary feed from 1 year of age.