The FAN bedding recovery system consists of a solid separator and an in-vessel aerobic composting system, allowing the treatment of dairy manure into separate liquid and solid streams, with the solid stream later used within the barn as dairy cows bedding. The objective was to evaluate the effect of composting on the microbiota profile and pathogen load of recovered bedding material (RBM). Manure (MAN), liquid stream (LS), solid stream undigested (SSU) and solid stream digested (SSD) samples were collected on a weekly basis for a 2-mo period during summer and winter seasons (n = 36/category). Genomic DNA was extracted and subjected to bacterial 16S rRNA gene sequencing for community analysis and qPCR for absolute quantification of generic Escherichia coli, E. coli O157:H7, Staphylococcus aureus, Mycobacterium avium ssp. paratuberculosus (MAP); Arcanobacterium pyogenes, and Klebsiella pneumonia. On average, 29,982 high-quality sequences were generated per sample. The α-diversity of SSD microbial communities was found to be lower (P < 0.001) than other treatment groups, with the MAN samples showing the most diverse microbiota followed by LS and SSU. The proportion of phylum Firmicutes (members of the family Bacillaceae) was greater (P < 0.05) in SSD group, and the relative abundances of several members of the phyla Proteobacteria (family Moraxellaceae and genus Acinetobacter) and Bacteroidetes (family Sphingobacteriaceae) were found to be significantly (P < 0.05) higher in SSU compared with other groups. The proportions of several members of the phylum Proteobacteria were also found to be higher in SSU compared with LS, suggesting that, in the absence of composting process, separation of the solid and liquid part of the RBM may increase the proportion of the opportunistic microorganism in the solid fraction. E. coli O157:H7, MAP and S. aureus were present only in a limited number of samples and only 2 SSD samples found to be MAP, O157:H7 or S. aureus positive. Aerobic composting had limited effect on the population of E. coli, A. pyogenes, and K. pneumonia.