Doping has the potential to alter the levels of anharmonicity in compounds by attenuating bonding strength. In this study, we explore the efficacy of amphoteric Al doping for stimulating anharmonicity in n-type Mg3.25AlxSb1.48Bi0.48Te0.04 to attain enhanced phonon scattering and thermoelectric performance. First-principles calculations and experimental data reveal the occupation of both Sb and Mg2 sites by amphoteric Al atoms in the anionic framework of Mg3.25AlxSb1.48Bi0.48Te0.04. A marginal variation in both carrier concentration and mobility sustains the high power factor without affecting the Seebeck coefficient, implying amphoteric doping induced charge compensation. While phonon velocity, Grüneisen parameter, and crystal orbital Hamilton population calculations results indicate that phonon softening and bond weakening are realized via Al doping, leading to an enhanced lattice anharmonicity and a reduced lattice thermal conductivity. A remarkable enhancement ∼16% in the peak figure of merit ZTpeak and the average ZTavg, was attained for the x = 0.015 sample, when compared with the un-doped sample. Hence, the amphoteric doping can serve as an effective means to optimize ZT values by decoupling the intertwined thermoelectric transport properties.