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Higher manganese silicides (HMSs) have emerged as promising candidates for environmentally friendly thermoelectric (TE) materials due to their earth-abundant and non-toxic composition. We report grain boundary engineering in ruthenium-doped HMSs via a melt-quenching followed by annealing method. This approach promotes the formation of MnSi nanoprecipitates and nanopores, preferentially near grain boundaries. The presence of these nanostructures results in a weak temperature-dependent thermal conductivity, resembling glass-like thermal transport behavior. A two-channel model incorporating propagons and diffusons describes this glass-like thermal conductivity, with diffusons contributing about 60 % of the lattice thermal conductivity at 300 K. Furthermore, the quench-annealing process enhances electrical conductivity while preserving a large Seebeck coefficient, which is attributed to a high density-of-states effective mass. As a result of improved power factor and reduced thermal conductivity, the figure of merit zT value increases by 33 % at 300 K compared to undoped HMS synthesized via solid-state reaction. These findings present a promising strategy for manipulating phonon dynamics in functional materials and designing efficient TE systems.