Xylella fastidiosa is one of the most destructive plant pathogenic bacteria worldwide, affecting more than 500 plant species. In Apulia region (southeastern Italy), X. fastidiosa subsp. pauca (Xfp) is responsible for a severe disease, the olive quick decline syndrome (OQDS), spreading epidemically and with dramatic impact on the agriculture, the landscape, the tourism, and the cultural heritage of this region. An early detection of the infected plants would hinder the rapid spread of the disease. The main objective of this paper was to define a geostatistical approach of data fusion, which combines remote (radiometric), and proximal (geophysical) sensor data and visual inspections with plant diagnostic tests, to provide probabilistic maps of Xfp infection risk. The study site was an olive grove located at Oria (province of Brindisi, Italy), where at the time of monitoring (September 2017) only few plants showed initial symptoms of the disease. The measurements included: 1) acquisitions of reflected electromagnetic radiation with UAV (Unmanned Aerial Vehicle) equipped with a multi-spectral camera; 2) geophysical surveys on the trunks of 49 plants with Ground Penetrating Radar (GPR); 3) disease severity rating, by visual inspection of the proportion of canopy with symptoms; 4) qPCR (real time-quantitative Polymerase Chain Reaction) data from tests on 61 plants. The data were submitted to a set of processing techniques to define a “data fusion” procedure, based on non-parametric multivariate geostatistics. The approach allowed marking those areas where the risk of infection was higher and identifying the possible infection entry routes into the field. The probability map of infection risk could be used as an effective tool for a preventive action and for a better organization of the monitoring plans.