Epitaxial ultrathin films are of utmost importance for state-of-the-art nanoelectronic devices, such as MOSFET transistors and non-volatile memories. At the same time, as the film thickness is reduced to a few nanometers, characterization of the materials is becoming challenging for commonly used methods. In this report, we demonstrate an approach for in-situ characterization of phase transitions of ultrathin nickel silicides using 3D medium-energy ion scattering. The technique provides simultaneously depth-resolved composition and real-space crystallography of the silicide films using a single sample and with a non-invasive probe. We show, for 10 nm Ni films on Si, that their composition follows a normal transition sequence, such as Ni-Ni2Si-NiSi. However, the transition process is significantly different for samples with initial Ni thickness of 3 nm. Depth-resolved crystallography shows that the Ni films transform from an as-deposited disordered layer to an epitaxial silicide layer at the temperature of ~290 °C, significantly lower than previously reported. The high depth resolution of the technique permits us to determine the composition of the ultrathin films to be 38% Ni and 62% Si.