Controlling the spatial distribution of functional groups on two-dimensional (2D) materials on a micrometer scale and below represents a fascinating opportunity to achieve anisotropic (opto)electronic properties of these materials. Periodic patterns of covalent functionalization can lead to periodic potentials in the monolayer; however, creating such superstructures is very challenging. Here, we describe an original approach to the periodic functionalization of graphene induced by substrate patterning using a pulsed laser. Laser-induced periodic surface structures (LIPSS) are produced on silicon wafers with thermally-grown oxide layers. The irradiation conditions for the formation of LIPSS confined at the SiO₂/Si interface have been unravelled. LIPSS imprint their periodicity to the reactivity of the monolayer graphene placed on the substrate via modulation of its local doping level. This method is clean, straightforward and scalable with high spatial resolution.