We study in-gap states of a single magnetic impurity embedded in a honeycomb monolayer which is deposited on superconducting substrate. The intrinsic spin–orbit coupling induces the quantum spin Hall insulating (QSHI) phase gapped around the Fermi energy. Under such circumstances we consider the emergence of Shiba-like bound states driven by the superconducting proximity effect. We investigate their topography, spin-polarization and signatures of the quantum phase transition manifested by reversal of the local currents circulating around the magnetic impurity. These phenomena might be important for more exotic in-gap quasiparticles in such complex nanostructures as magnetic nanowires or islands, where the spin–orbit interaction along with the proximity induced electron pairing give rise to topological phases hosting the protected boundary modes.