Online extraction of fission products, such as the medical isotope Mo-99, is a key advantage of the proposed molten salt nuclear reactor design. The chemical and structural behavior of Mo solvated in fluoride salt has been relatively unknown. Ab initio molecular dynamics simulations were employed to examine the behavior of molybdenum in the molten salt FLiNaK (LiF-NaF-KF) for oxidation states between 0 and 6+. Mo complexation was found to vary with the Mo oxidation state, with lower oxidation states tending to result in complexes with more molybdenum ions. Complexes containing multiple Mo ions were observed for all Mo oxidation states studied except 5+ and 6+. A relationship between the solubility of a complex and electronic isolation of a complex in a molten salt is explored using the Bader atoms in molecule electron density partitioning scheme, with more volatile complexes exhibiting greater electronic isolation. The impacts of UF4 and H2O on the predominant molybdenum species are also considered. While no impacts on Mo behavior by UF4 were observed, Mo–O interactions may inhibit the formation of complexes containing multiple Mo ions.