In this study, we propose grain boundary engineering and nanostructuring to enhance the thermoelectric performance of SnTe through tri-doping with Mn, Ge, and Bi. The synergistic effects on the band structure were analyzed through DFT calculations and validated through a series of doping experiments with each dopant. The nonstoichiometrically tri-doped sample exhibits a unique microstructure, characterized by Mn—Ge precipitates along the grain boundaries and coherently embedded nanostructures within the matrix. These microstructural features, combined with the effects of each dopant, synergistically enhanced the thermoelectric properties, yielding a maximum zT of 1.32 at 873 K. The thermoelectric generator exhibited a maximum output power of 661 μW at ΔT = 485 K, confirming its viability for mid-temperature thermoelectric applications.