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Abstract The functionality of atomic quantum emitters is intrinsically linked to their host lattice coordination. Structural distortions that spontaneously break the lattice symmetry strongly impact their optical emission properties and spin-photon interface. Here we report on the direct imaging of charge state-dependent symmetry breaking of two prototypical atomic quantum emitters in mono- and bilayer MoS₂by scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM). By changing the built-in substrate chemical potential, different charge states of sulfur vacancies (Vac_S) and substitutional rhenium dopants (Re_Mo) can be stabilized.$${\mathrm{Vac}}_{{{{{{{{\rm{S}}}}}}}}}^{-1}$$ ${\mathrm{Vac}}_S^{-1}$as well as$${{\mathrm{Re}}}_{{{{{{{{\rm{Mo}}}}}}}}}^{0}$$ ${\mathrm{Re}}_{\mathrm{Mo}}^0$and$${\mathrm{Re}}_{{\rm{Mo}}}^{-1}$$ ${\mathrm{Re}}_{\mathrm{Mo}}^{-1}$exhibit local lattice distortions and symmetry-broken defect orbitals attributed to a Jahn-Teller effect (JTE) and pseudo-JTE, respectively. By mapping the electronic and geometric structure of single point defects, we disentangle the effects of spatial averaging, charge multistability, configurational dynamics, and external perturbations that often mask the presence of local symmetry breaking.