Cu$_2$Se is a mixed ionic-electronic conductor with outstanding thermoelectric performance originally envisioned for space missions. Applications were discontinued due to material instability, where elemental Cu grows at the electrode interfaces during operation in vacuum. Here, we show that when Cu$_2$Se is operating in air, formation of an oxide surface layer suppresses Cu$^+$ migration along the current direction. In operando X-ray scattering and electrical resistivity measurements quantify Cu$^+$ migration through refinement of atomic occupancies and phase composition analysis. Cu deposition can be prevented during operation in air, irrespective of a critical voltage, if the thermal gradient is applied along the current direction. Maximum entropy electron density analysis provides experimental evidence that Cu$^+$ migration pathways under thermal and electrical gradients differ substantially from equilibrium diffusion. The study establishes new promise for inexpensive sustainable Cu$_2$Se in thermoelectric applications, and it underscores the importance of atomistic insight into materials during thermoelectric operating conditions.
