Digital inkjet printing is a production technology with high potential in resource efficient processes, which features both flexibility and productivity. In this research, waterborne, fluorocarbon-free ink containing polysiloxane in the form of micro-emulsion is formulated for the application of water-repellent sports- and work wear. The physicochemical properties of the ink such as surface tension, rheological properties and particle size are characterized, and thereafter inkjet printed as solid square pattern (10 × 10 cm) on polyester and polyamide 66 fabrics. The water contact angle (WCA) of the functional surfaces is increased from < 90° to ca. 140° after 10 inkjet printing passes. Moreover, the functional surface shows resistance to wash and abrasion. The WCA of functional surfaces is between 130° and 140° after 10 wash cycles, and is ca. 140° after 20000 revolutions of rubbing. The differences in construction of the textile as well as ink–filament interaction attribute to the different transportation behaviors of the ink on the textile, reflected in the durability of the functional layer on the textile. The functionalized textile preserves its key textile feature such as softness and breathability. Inkjet printing shows large potential in high-end applications such as customized functionalization of textiles in the domain of smart textiles.