Xylella fastidiosa subsp. pauca (Xfp) is associated with olive quick decline syndrome (OQDS), a severe disease affecting the olive groves of Salento (Apulia, Italy). Through a series of interdisciplinary studies, an effective management strategy aimed at maintaining the traditional olive germplasm has been developed and evaluated. Specifically, a systemic biocomplex formulation containing zinc (4%), copper (2%) and citric acid, is sprayed on the tree canopy once per month from spring to early autumn. The strategy also includes sustainable vector control through agronomical techniques as well as regular tree pruning and soil fertilization. Quantitative real-time PCR assessments performed in a mid- and long-term studies showed a significant reduction in the Xfp concentration in the leaf xylem tissue upon treatment, improving olive tree yield. Both 1H-NMR metabolomic and mass spectrometric lipidomic analyses of leaf extracts revealed the occurrence of biomarkers linked to disease or tree restoration. The effects of mannitol and oleuropein derivatives, 13-oxylipins/DOX-oxylipins and 9-oxylipins appear to be related to the attenuation of disease symptoms. Both techniques indicate rapid reprogramming of metabolic tree activity upon spray treatment to regain tree health. Multiscale satellite imagery monitoring through high-resolution Sentinel-2, very high-resolution Pleiades and vegetation indices confirmed the robustness of the strategy over several years in both experimental and productive olive groves. Currently, this strategy is applied in many infected olive groves in Salento. Notably, some aggressive fungal species belonging to the Neofusicoccum genus have been recently found to be associated with olive trees that show symptoms similar to those induced by Xfp. Coinfections between this bacterium and fungi have also been frequently observed, suggesting the need for a more in-depth assessment of the epidemiology and management of OQDS.