The Monastery of Varnakova is one of the most important and oldest religious complexes in Greece with high historical significance. The Catholicon was reconstructed in 1831 on the remains of the 11th century structure. Today it is in a bad state of preservation, as it has been severely affected by strong earthquakes and presents serious problems regarding both its stability and aesthetic values. Because of the importance of the monument and taking into account its poor state of preservation, a thorough diagnostic study was conducted through an interdisciplinary approach, which involved historical, architectural and structural analysis, as well as materi-als characterization and diagnosis of decay patterns, in order to propose an optimized rehabilitation plan. Techniques used included a 3D laser scanning and photogrammetric techniques, UAV images, a Total Station survey, 3D textured model using various techniques and software, prospection by ground penetrating radar (GPR), infrared thermography (IRT), finite element (FE) software, X-ray diffraction (XRD), Differential Ther-mal and Thermo-Gravimetric Analysis (DTA-TG), polarized light microscope examination, structural and me-chanical properties for material restoration (e.g. stones and mortars), as well as historical stone mechanical strength tests. The history and description of the monument are presented, while the preservation state and the risks that are imposing the need for restoration, as well as the conceptual proposal of restoration, follow the pathology and decay diagnosis of the monument. Digital documentation permits the fusion of the various disciplines’ data, hence allowing for the integrated design of interventions. The dynamics of the digital recon-struction allow for the adjustment of the restoration process according to the findings. Thus, the rehabilitation plan, which has initiated, takes into account and combines the findings of all scientific fields and proposes the use of new compatible and performing restoration materials and appropriate rehabilitation actions, capable of ensuring structural integrity and highlighting the values of this important monument, within an innovative project management scheme and in a dynamic manner, throughout the implementation of the project. This is an exemplary work transferring the model of the Rehabilitation of the Holy Aedicule project to Greece, based on a transdisciplinary approach and multi-actors’ cooperation.