Skim milk was microfiltered in a pilot system equipped with ceramic membranes that have a novel configuration in their active layer, for the production of microbiologically-stable milk. The linear velocity (LV), temperature (T), and transmembrane pressure (TMP) were studied to assess the effect on bacterial reduction and protein permeation in the microfiltration system. Statistical analysis showed significant effects (α = 0.05) of T on flux, LV on protein permeation, and all the three conditions on the logarithmic reduction of microorganisms. The optimal operational conditions in the system obtained by the surface response method were LV = 6 m/s, T = 30 C, and TMP = 1.5 bar. These operational conditions ensured high filtration performance and a logarithmic reduction of bacteria by 4.55 log and extension of the shelf life to 5 days during storage at 4 C, the microbiological stability of microfiltered milk was not affected by the addition of prebiotic agave fructans of a high degree of polymerization. The microfiltration allows microbiological stability, conservation of functional compounds, and preservation of organoleptic sensory properties of milk, for the production of healthy and innocuous fresh dairy products with higher shelf life.