We analyze the effect of weak localization (WL) and weak antilocalization (WAL) in the electronic transport through HgTe/CdTe quantum wells. We show that for increasing Fermi energy, the magnetoconductance of a diffusive system with inverted band ordering features a transition from WL to WAL and back, if spin–orbit interactions from bulk and structure inversion asymmetries can be neglected. This, and an additional splitting in the magnetoconductance profile, is a signature of the Berry phase arising for inverted band ordering and is not present in heterostructures with conventional ordering. In the presence of spin–orbit interaction, both band topologies exhibit WAL, which is distinctly energy dependent for quantum wells with inverted band ordering. This can be explained by an energy-dependent decomposition of the Hamiltonian into two blocks.