Data paper is available at https://doi.org/10.1016/j.dib.2021.107063. Milk microfiltration process plays a key role in the dairy in- dustry. Crossflow microfiltration of skimmed milk using a membrane with 0.1 μm mean pore size is widely used to fractionate the two main groups of dairy proteins: casein mi- celles (~150 nm) and serum proteins (~2-15 nm). Retentate, containing mainly casein micelles, is generally used to en- rich vat milk for cheese making. Permeate, containing serum proteins, lactose and minerals, is usually ultrafiltered in or- der to produce protein-rich concentrate with a high nutri- tional value dedicated to specific populations such as infants and seniors. The great interest in these protein fractions ex- plains the increasing number of microfiltration equipments in the dairy industry. This data article contains data as- sociated with milk microfiltration process experiments and properties of the resulting dairy fractions annotated from a collection of scientific documents. These data are stored in INRAE public repository (see Data accessibility in the Spec- ification Table for direct links to data). They have been structured using MILK MICROFILTRATION ontology and are replicated in @Web data warehouse providing additional querying tools ( https://www6.inrae.fr/cati- icat- atweb/ ).