In the Western Alps, the ocean-derived Lago di Cignana Unit of the Piemonte Zone has experienced ultrahigh-pressure metamorphism. We have studied the minerals of two eclogite samples from this unit using transmission electron microscopy (TEM) in order to characterise their microstructures. These microstructures are the result of deformation, phase transformation and reactions and allow conclusions on the processes that had generated them. The goal of this process-oriented paper is to contribute to the knowledge of the formation and exhumation of ultrahigh pressure eclogites. In our TEM-study we found omphacite, amphibole (barroisite, glaucophane, hornblende), clinozoisite, garnet, albite, and thin layers of chlorite and mica in amphibole. The omphacite is well-ordered and has the space-group P2/n. We observed antiphase domains (APDs), dislocations that are organised in small-angle grain boundaries, and – very rare – crystallographic shear planes parallel to (010) and (110). Deformation twin lamellae on (100) have not been observed. Most interesting is the first observation of faults parallel to (110) in a natural omphacite. They are due to deformation. Chain multiplicity faults are common in the amphibole grains. In one case, the orientation of crystallographic shear planes was not only parallel to (010), but also parallel to (130) and (− 110). Clinozoisite showed deformation twin lamellae on (100) with widths of a few nm up to about 50 nm. Dislocations organised into a small-angle grain boundary have been found, which have not been described before. The garnet is almost free of dislocations. While there are differences regarding the deformation microstructures from the UHP Lago di Cignana eclogite and other HP occurrences, it is unlikely that these are due to higher pressures. It is much more likely that the whole formation and exhumation history of the different geological units and the individual positions of the collected rocks within them are reflected in their microstructures. A tentative correlation of the omphacite microstructures with the P–T path of the Lago di Cignana Unit is presented. An important point is the early crystallisation of C2/c-omphacite at a temperature below 500 °C, perhaps around 400 °C. The low temperature prevents rapid diffusion-controlled ordering to P2/nomphacite and thus enables deformation of the metastable C2/c-omphacite. Since C2/c-omphacite is more easily to deform than P2/n-omphacite, this may influence the interplate coupling. The onset of the transition to P2/n-omphacite, however, will increase the shear strength of eclogite and the coupling with the overriding plate, which may slow-down the subduction and finally stop it.