In this manuscript we review our recent work on the structure and dynamics of iron and cobalt complexes with macrocyclic ligands using ab initio molecular dynamics (AIMD). AIMD techniques are used to analyze the short time scale dynamics of these complexes, helping to understand the results obtained by experimental methods with larger time resolution. Firstly, the case of the iron–oxygen bond in myoglobin (Mb) and hemoglobin (Hb), as well as its cobalt analogues, will be discussed. Secondly, we will focus on the B12 coenzyme and its organocobaloxime derivatives. The simulations grasp the role played by temperature on the dynamics of ligands (the FeO2 and CoO2 moieties in heme models and the bridging OH⋯O protons in organocobaloxime crystals), clarifying problems related to average structures and underscoring the need to perform dynamical simulations.