Understanding the dielectric loss mechanisms in microwave ceramics is important since losses can hinder its applications. Cr, Fe and Co containing MgTiO3 ceramics were prepared using a high purity powder obtained by a chemical route. Single-phase materials were obtained for all doped ceramics with the exception of the slowly cooled Fe-doped samples in which a surface layer of MgTi2O5 was detected, containing a higher concentration of the dopant. The relationship between the obtained microstructures and the microwave dielectric properties is discussed. The main variations are observed in the dielectric loss which is affected by doping and processing parameters. Anharmonicity of lattice vibration modes caused by point defects and linear defects is suggested as responsible for the higher losses.