The mechanism of the trans to cis isomerization in Ru complexes with a chelating alkylidene group has been investigated by using a combined theoretical and experimental approach. Static DFT calculations suggest that a concerted single-step mechanism is slightly favored over a multistep mechanism, which would require dissociation of one of the ligands from the Ru center. This hypothesis is supported by analysis of the experimental kinetics of isomerization, as followed by (1)H NMR spectroscopy. DFT molecular dynamics simulations revealed that the variation of geometrical parameters around the Ru center in the concerted mechanism is highly uncorrelated; the mechanism actually begins with the transformation of the square-pyramidal trans isomer, with the Ru==CHR bond in the apical position, into a transition state that resembles a metastable square pyramidal complex with a Cl atom in the apical position. This high-energy structure collapses into the cis isomer. Then, the influence of the N-heterocyclic carbene ligand, the halogen, and the chelating alkylidene group on the relative stability of the cis and trans isomers, as well as on the energy barrier separating them, was investigated with static calculations. Finally, we investigated the interconversion between cis and trans isomers of the species involved in the catalytic cycle of olefin metathesis; we characterized an unprecedented square-pyramidal metallacycle with the N-heterocyclic carbene ligand in the apical position. Our analysis, which is relevant to the exchange of equatorial ligands in other square pyramidal complexes, presents evidence for a remarkable flexibility well beyond the simple cis-trans isomerization of these Ru complexes.