X-ray diffraction is measured on individual bilayer and multilayer graphene single-crystals and combined with electrochemically induced lithium intercalation. In-plane Bragg peaks are observed by grazing incidence diffraction. Focusing the incident beam down to an area of about 10 μm × 10 μm, individual flakes are probed by specular X-ray reflectivity. By deploying a recursive Parratt algorithm to model the experimental data, we gain access to characteristic crystallographic parameters of the samples. Notably, it is possible to directly extract the bi/multilayer graphene c-axis lattice parameter. The latter is found to increase upon lithiation, which we control using an on-chip peripheral electrochemical cell layout. These experiments demonstrate the feasibility of in situ X-ray diffraction on individual, micron-sized single crystallites of few- and bilayer two-dimensional materials.