In energy dispersive X-ray fluorescence (EDXRF) analytical studies of samples, the absorption and enhancement of analyte X-rays, collectively called matrix effects, complicate the relation between intensity of analyte X-rays and its concentration. Earlier, the absorption and enhancement relative terms have been derived from the built-up experimental relations of analyte X-ray counts with XRF fundamental parameters and the parameters of the experimental set-up for each selective and enhanced X-rays. Now, the terms are implemented on the determined amounts of potassium and calcium nutrients in plants and pot soils from an experiment performed in the lab by growing fenugreek plants on the soils with variable contamination levels and applied fertilizers. The variation pattern of the terms with respective nutrient contents is found to be affected by the basic nature of soils. The pattern shows the high sensitivity of the terms to the plant's behaviour in soil and reflects the picture of supressed benefits of applied fertilizers to the heavy-metals contaminated soils.