Archival resources, a photogrammetric survey, analysis of materials and techniques, and evaluation of the state of conservation were interconnected phases in the interdisciplinary research on the perspective scenery of the Teatro Olimpico in Vicenza. To fill existing gaps related to the history of this unique artefact and to the undocumented retouching of paint layers on the scenery during post-war reconstruction work, a broad analytical approach (optical microscopy, XRPD, SEM–EDX, μFTIR and μRaman) was applied to micro-samples, the selection of which was guided by consolidated geometrical and archival data. The aims were to obtain a characterisation of the pigments and binders and to evaluate the microstratigraphic sequence, the state of conservation of the scenery flats, and the deterioration processes involved. The findings unveiled a discernible variability in the production techniques of the finishes, frequently lacking the classic microstratigraphic sequence associated with the traditional method for painting on wooden panels from the sixteenth century. Moreover, by identifying many pigments that could be used as temporal markers we were able unequivocally to establish, for the first time, that a significant part of the scenery designed by the architect Vincenzo Scamozzi was heavily repainted in the post-WWII period. These analytical results and all the data collected on the artefacts over time were related through an HBIM model, enabling the historical and technical-analytical information to be linked to the geometrical survey and thus to provide guidance for actions based on current and future knowledge for the maintenance and monitoring of the Teatro Olimpico.