The successful use of energy-dispersive X-ray fluorescence (ED-XRF) sensors for soil analysis requires the selection of an optimal procedure of data acquisition and a simple modelling approach. This work aimed at assessing the performance of a portable XRF (XRF) sensor set up with two different X-ray tube configurations (combinations of voltage and current) to predict nine key soil fertility attributes: (clay, organic matter (OM), cation exchange capacity (CEC), pH, base saturation (V), and extractable nutrients (P, K, Ca, and Mg). An XRF, operated at a voltage of 15 kV (and current of 23 μA) and 35 kV (and current of 7 μA), was used for analyzing 102 soil samples collected from two agricultural fields in Brazil. Two different XRF data analysis scenarios were used to build the predictive models: (i) 10 emission lines of 15 keV spectra (EL-15), and (ii) 12 emission lines of 35 keV spectra (EL-35). Multiple linear regressions (MLR) were used for model calibration, and the models’ prediction performance was evaluated using different figures of merit. The results show that although X-ray tube configuration affected the intensity of the emission lines of the different elements detected, it did not influence the prediction accuracy of the studied key fertility attributes, suggesting that both X-ray tube configurations tested can be used for future analyses. Satisfactory predictions with residual prediction deviation (RPD) ≥ 1.54 and coefficient of determination (R2) ≥ 0.61 were obtained for eight out of the ten studied soil fertility attributes (clay, OM, CEC, V, and extractable K, Ca, and Mg). In addition, simple MLR models with a limited number of emission lines was effective for practical soil analysis of the key soil fertility attributes (except pH and extractable P) using XRF. The simple and transparent methodology suggested also enables future researches that seek to optimize the XRF scanning time in order to speed up the XRF analysis in soil samples.