Phase relations in Cr3S4 and the substituted system Cr3S4–x Se x are studied to determine the influence of chemical substitutions on the thermoelectric properties. In addition to the expected equilibrium phase crystallizing in the monoclinic space group I2/m, some samples exhibit a defect phase with Cr2S3‐like structure. The defect phase can be observed in a few samples prior to sintering, with the majority being phase‐pure Cr3S4. The defect phase can, however, be introduced in phase‐pure samples through in situ heating. It can be proven that the defect phase has an influence on the thermoelectric properties, by lowering the electrical and thermal conductivity, while increasing the Seebeck coefficient. Substitution in the anion lattice of Cr3S4 with Se lowers the thermal conductivity. The improvement is mainly achieved through a reduction of the electronic contribution to the thermal conductivity, leading to total values as low as 1.6 Wm−1 K−1 for the substituted system in comparison to the pristine material 2.3 Wm−1 K−1. Herein, phase relations in Cr3S4 and the substituted system Cr3S4–x Se x are studied. A defect phase occurs that exhibits a Cr2S3‐like crystal structure but retains the stoichiometry of Cr3S4. Electrical and thermal conductivities are affected and both are lowered by the inclusion of the defect phase. Anion substitution with Se suppresses the defect phase and lowers the thermal conductivity.