Membrane filtration technologies are the best available tools to manage dairy byproducts such as cheese whey, allowing for the selective concentration of its specific components, namely proteins. Their acceptable costs and ease of operation make them suitable for application by small/medium-scale dairy plants. The aim of this work is the development of new synbiotic kefir products based on sheep and goat liquid whey concentrates (LWC) obtained by ultrafiltration. Four formulations for each LWC based on a commercial kefir starter or traditional kefir, without or with the addition of a probiotic culture, were produced. The physicochemical, microbiological, and sensory properties of the samples were determined. Membrane process parameters indicated that ultrafiltration can be applied for obtaining LWCs in small/medium scale dairy plants with high protein concentration (16.4% for sheep and 7.8% for goats). Sheep kefirs showed a solid-like texture while goat kefirs were liquid. All samples presented counts of lactic acid bacteria higher than log 7 CFU/mL, indicating the good adaptation of microorganisms to the matrixes. Further work must be undertaken in order to improve the acceptability of the products. It could be concluded that small/medium-scale dairy plants can use ultrafiltration equipment to valorize sheep’s and goat’s cheese whey-producing synbiotic kefirs.