Goat milk shows interesting similarities in comparison with human milk in terms of their oligosaccharides composition, which suggests that goat milk oligosaccharides could mimic the physiological activities described for human milk oligosaccharides. However, the supplementation of the accompanying goat milk protein in infant formulae is not allowed by the current European legislation. The purpose of this study was to evaluate the potential use of a 50 kDa tubular ceramic membrane in the production of goat milk permeates with a reduced content in protein, while recovering the whole oligosaccharide fraction. The continuous diafiltration process devised was able to recover 95% of the oligosaccharides and to retain 94% of the protein after the 3 diavolumes filtered in 12.3 h of operation. A dynamic model consisting in a system of differential and algebraic equations was able to reproduce the experimental data and was further useful in order to determine the minimum number of membrane modules needed to achieve a required recovery of oligosaccharides.