Computational methods can help in the design of new bioorganometallic compounds. However, the presence of multihapto or σ/π metal‐ligand bonding still precludes the direct application of either pure molecular mechanics (MM) or hybrid quantum mechanics‐MM methods to study the flexibility of biomolecules in complex with organometallics. Herein, we present a computational protocol aimed to the evaluation of the relative free energies of bioorganometallic compounds, which explores the conformational space by means of Molecular Dynamics simulations using the semiempirical PM6 method coupled with the COnductor‐like Screening MOdel solvation model followed by density functional theory (DFT) calculations including the DFT‐D3 dispersion energy correction on the most stable conformers. This protocol is applied to investigate the complexes formed between cysteine and the molybdocene entity Cp2Mo2+ (Cpη5C5H5), which has received considerable attention due to its potential antitumor activity and