Machine Learning (ML) algorithms have been used for assessing soil quality parameters along with non-destructive methodologies. Among spectroscopic analytical methodologies, energy dispersive X-ray fluorescence (EDXRF) is one of the more quick, environmentally friendly and less expensive when compared to conventional methods. However, some challenges in EDXRF spectral data analysis still demand more efficient methods capable of providing accurate outcomes. Using Multi-target Regression (MTR) methods, multiple parameters can be predicted, and also taking advantage of inter-correlated parameters the overall predictive performance can be improved. In this study, we proposed the Multi-target Stacked Generalisation (MTSG), a novel MTR method relying on learning from different regressors arranged in stacking structure for a boosted outcome. We compared MTSG and 5 MTR methods for predicting 10 parameters of soil fertility. Random Forest and Support Vector Machine (with linear and radial kernels) were used as learning algorithms embedded into each MTR method. Results showed the superiority of MTR methods over the Single-target Regression (the traditional ML method), reducing the predictive error for 5 parameters. Particularly, MTSG obtained the lowest error for phosphorus, total organic carbon and cation exchange capacity. When observing the relative performance of Support Vector Machine with a radial kernel, the prediction of base saturation percentage was improved in 19%. Finally, the proposed method was able to reduce the average error from 0.67 (single-target) to 0.64 analysing all targets, representing a global improvement of 4.48%.