Type I clathrates have recently been identified as prospective thermoelectric materials for power generation purposes due to their very low lattice thermal conductivity values. The maximum thermoelectric figure of merit of almost all type I clathrates is, however, less than 1 and occurs at, or above, 1000 K, making them unfavorable especially for intermediate temperature applications. In this report, the Zintl–Klemm rule is demonstrated to be valid for Ni, Cu, and Zn transition metal substitution in the framework of type I clathrates and offers many degrees of freedom for material modification, design, and optimization. The cross-substitution of framework elements introduces ionized impurities and lattice defects into these materials, which optimize the scattering of charge carriers by the substitution-induced ionized impurities and the scattering of heat-carrying lattice phonons by point defects, respectively, leading to an enhanced power factor, reduced lattice thermal conductivity, and therefore improved thermoelectric figure of merit. Most importantly, the bandgap of these materials can be tuned between 0.1 and 0.5 eV by adjusting the cross-substitution ratio of framework elements, making it possible to design clathrates with excellent thermoelectric properties between 500 and 1000 K.