Mammary inflammation, known as mastitis, is a major constraint to milk production and quality. Previous research suggests that changes in the bacterial composition of bovine milk are associated with changes in mammary inflammation, and are influenced by factors such as a cow’s parity and farm management, which includes bedding material used. A goal of this research was to find evidence in support of this notion. To achieve this, a cross-sectional study was carried out to compare bacterial diversity of aseptically sampled milk from cows (n = 137) in different parities (multiparous vs. primiparous) housed on 3 farms each using a different bedding material [sand (SA), straw (ST), and recovered bedding material (RBM)]. Composite milk somatic cell count (SCC) was measured and used as an indicator of mammary inflammation. A β-diversity analysis using UniFrac distances reviled that milk microbial communities were distinct between farms (P_(PERMANOVA) < 0.0001) and parities (P_(PERMANOVA) = 0.045). In addition, fewer bacterial species were identified in milk of primiparous compared with multiparous cows (Chao1 index, P < 0.05); also, fewer bacterial species were identified in milk from farm ST compared with the other farms (Chao1 index, P < 0.05). The predominant phyla identified, Proteobacteria, was proportionally more abundant (q_(FDR) < 0.0001) in farm ST (72 ± 19.0) compared with farm SA (50 ± 20.5%) and farm RBM (51 ± 21.7%). Furthermore, within farms ST and SA, milk SCC was positively correlated with the proportion of Staphylococcus. On farm ST only, milk SCC was also negatively correlated with the proportion of some genera (Methylobacterium, Ralstonia, unclassified Betaproteobacteria, unclassified Comamonadaceae and unclassified Rhodospirillaceae) indicating potential for these microbiota to help limit mammary inflammation. While cows sampled from farm RBM had a higher SCC than the other 2 farms (P < 0.05), no genera could be correlated with milk SCC for this farm. Our results are in support of the idea that there are between-farm differences in milk bacterial diversity and in how milk microbiota are associated with mammary inflammatory status.