Herein, we report the effects of indium (In) incorporation upon the thermoelectric and magnetic properties of Ni doped Fe-based filled skutterudites (InxCe0.9Fe3.5Ni0.5Sb12 with x = 0, 0.1, and 0.5). We find that secondary phases (such as InSb) can be formed upon surpassing the filling fraction limit and these in turn result in improved thermoelectric properties. A maximum dimensionless figure of merit, ZT ≈ 0.9 at ∼650 K was obtained for the sample with the nominal composition In0.1Ce0.9Fe3.5Ni0.5Sb12. Interestingly, we also observe Kondo-like behavior and evidence of the crystal field effect in these samples. The low-temperature (T < 100 K) thermopower and electrical resistivity of our samples exhibit Kondo-like behavior while their corresponding magnetic susceptibility suggests that the Ce3+ ions are influenced by the cubic crystal symmetry of the skutterudites class of materials, thus resulting in the crystal field effect. Lastly, the magnetic susceptibility data can be interpreted in the context of a second-order perturbation model.