The two-dimensional XRD (GADDS) was used to characterize the microstructure of an applied self-leveling compound (SLC). A calcium aluminate cement based SLC was prepared on two different substrates (water absorbent and nonwater absorbent) to determine the vertical distribution of the crystalline phases. The application of the GADDS enables the detection of the phase composition of the hydrating mortar in horizontal slices. Thus the analysis could be carried out in position-sensitive mode at three different areas: near the bottom, in the center, and at the top of the mortar. For investigation of SLCs from the very early hydration stage up to 10 h of hydration, a custom-made in situ sample holder for the measurements was designed and constructed. The combination of the GADDS and the custom-made in situ sample holder provides the possibility to characterize additionally the time-dependent phase composition within the SLC. The nonabsorbent substrate has no effect on the hydration of the binder phases but the absorbent substrate influences the formation of ettringite. In the top layer of the SLC the ettringite content is reduced during the first hours of hydration. The absorbing forces of the substrate lead to migration of the mix water to the substrate. This lack of water results in the reduced formation of ettringite.