The existing building stock in several countries worldwide features masonry structures with timber floors, whose vulnerability to seismic events has been widely documented by academic research as well as by the catastrophic consequences of recent earthquakes. Several seismic retrofits and protection technologies have been explored throughout the years, prioritizing (among others) lightweight interventions, such as timber-based strengthening, or advanced systems involving seismic isolation and vibration control strategies (e.g. inter-story seismic isolation). The use of timber-based retrofits, particularly based on engineered wood panels fastened to existing floors and roofs, has shown to increase the hysteretic energy dissipation of these diaphragms, beneficially reducing seismic shear forces transferred to the walls when the strengthening measure is appropriately designed. Similarly, the seismic isolation of the masses localized at the roof level, can provide a strong reduction in shear loads on the walls, acting as a Tuned Mass Damper for the existing building. However, the calibration of the stiffness of the isolators still proves to be a critical subject, since the degradation of the masonry induced by the earthquake modifies the dynamic properties of the original structure, based on which the isolation system is designed, potentially reducing or cancelling its beneficial effect. On the basis of the described framework, this work examines a case-study archetype masonry building with a timber roof: by performing numerical analyses in OpenSees software, this study compares (i) the application of timber-based retrofitting solution on the roof, (ii) the use of an additional, superimposed roof structure acting as tuned mass damper with properly calibrated isolators, and (iii) the combination of the two systems, discussing the benefits and applicability of each seismic protection method and their integration with other retrofits, for instance from the energetic and environmental point of view.