Over the last 15 years, bulk hydrophobic treatment of cementitious materials with silanes and siloxanes is in the scientific focus. They are beneficial in terms of reducing water uptake by capillarity, however, this is often followed by an impact on cement hydration leading to the decrease in structural properties of cement matrix. The aim of this paper is to study the influence of different incorporation modes of a silicone-based hydrophobic agent used for the bulk hydrophobic treatment of mortars, and to evaluate their effect on cement hydration and the early age properties. Two different incorporation modes are compared: an emulsion of silane and silicone resin and microencapsulation of silicone resin. Each of these is incorporated in mortars prepared with CEM I and CEM III/A. Based on the combined measurement of isothermal calorimetry, electrical resistivity, ultrasonic pulse velocity, compressive strength, thermal expansion coefficient and autogenous deformation at early age, it is shown that the emulsion, as a delivery method of hydrophobic agent, affects the early age mechanical behavior of cement-based systems, for both types of cements. The microencapsulation on the other hand, prevents these effects from occurring, and is therefore suitable for bulk hydrophobic treatment.