The work aimed to discriminate among different soil management treatments in terms of beneficial effects by high-resolution thermal and spectral vegetation imagery using an unmanned aerial vehicle and open-source GIS software. Five soil management treatments were applied in two organic vineyards (cv. Sangiovese) from Chianti Classico terroir (Tuscany, Italy) during two experimental years. The treatments tested consisted of conventional tillage, spontaneous vegetation, pigeon bean (Vicia faba var. minor Beck) incorporated in spring, mixture of barley (Hordeum vulgare L.) and clover (Trifolium squarrosum L.) incorporated or left as dead mulch in late spring. The images acquired remotely were analyzed through map-algebra and map-statistics in QGIS and correlated with field ecophysiological measurements. The surface temperature, crop water stress index (CWSI) and normalized difference vegetation index (NDVI) of each vine row under treatments were compared based on frequency distribution functions and statistics descriptors of position. The spectral vegetation and thermal-based indices were significantly correlated with the respective leaf area index (R2 = 0.89) and stem water potential measurements (R2 = 0.59), and thus are an expression of the crop vigor and water status. The gravel and active limestone soil components determined the spatial variability of vine biophysical (e.g., canopy vigor) and physiological characteristics (e.g., vine chlorophyll content) in both farms. The vine canopy surface temperature, and CWSI were lower on the spontaneous and pigeon bean treatments in both farms, thus evidencing less physiological stress on the vine rows derived from the cover crop residual effect. In conclusion, the proposed methodology showed the capacity to discriminate across soil management practices and map the spatial variability within vineyards. The methodology could serve as a simple and non-invasive tool for precision soil management in rainfed vineyards to guide producers on using the most efficient and profitable practice.