Microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels. On ten farms our results indicated that the number of microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. The milk microbiota showed a farm-specific fingerprint. Repeated sampling of a farm showed that this fingerprint changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition. ; This dataset is already pre-processed and can be directly loaded in R using the phyloseq package. Note this data is not rarefied.