Despite that the chemistry of octahedral cluster complexes has been actively developed recently, there are still a lot of unexplored areas. For example, to date, only a few halide M6-clusters with N-heterocycles are known. Here, we obtained an apically heteroleptic octahedral iodide molybdenum cluster complex with pyridine ligands—trans-[{Mo6I8}(py)2I4] by the direct substitution of iodide apical ligands of [{Mo6I8}I6]2– in a pyridine solution. The compound co-crystalized with a monosubstituted form [{Mo6I8}(py)I5]– in the ratio of 1:4, and thus, can be described by the formula (pyH)0.2[{Mo6I8}(py)1.8I4.2]·1.8py. The composition was studied using XRPD, elemental analyses, and 1H-NMR and IR spectroscopies. According to the absorption and luminescence data, the partial substitution of apical ligands weakly affects optical properties.