The present invention concerns a process for producing compositions that are rich in secretory IgA (S-IgA) by fractionating milk containing S-IgA. Such compositions may be used in particular for treating and/or preventing infections and/or inflammation of the mucosal surfaces, e.g. the gastro-intestinal tract, urogenital tract, respiratory tract, nasal cavity or oral cavity, treating and/or preventing obesity and related diseases, or treating and/or preventing food allergies in subjects in need of such treatment. Briefly stated, the current invention provides a process for producing milk fractions rich in secretory Immunoglobulin A, using one or more microporous membrane filtration steps. A preferred protocol of the present process involves de-fatting, micro-filtration and ultrafiltration-concentration through a number of diafiltration cycles. The process of the invention, apart from the unexpectedly high yields achievable, offers advantages which are of particular interest in view of the scalability, application in existing diary factories and controllability of process parameters influencing the S-IgA quality and stability.