We discuss a pairing mechanism in interacting two-dimensional multipartite lattices that intrinsically leads to a second order topological superconducting state with a spatially modulated gap. When the chemical potential is close to Dirac points, oppositely moving electrons on the Fermi surface undergo an interference phenomenon in which the Berry phase converts a repulsive electron-electron interaction into an effective attraction. The topology of the superconducting phase manifests as gapped edge modes in the quasiparticle spectrum and Majorana Kramers pairs at the corners. We present symmetry arguments which constrain the possible form of the electron-electron interactions in these systems and classify the possible superconducting phases which result. Exact diagonalization of the Bogoliubov-de Gennes Hamiltonian confirms the existence of gapped edge states and Majorana corner states, which strongly depend on the spatial structure of the gap. Possible applications to vanadium-based superconducting kagome metals AV(3)Sb(5) (A = K, Rb, Cs) are discussed.