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Soil acidity is the most limiting factor for agricultural yield and sustainability in acid soils. Liming is the management practice recommended for reducing soil acidity and increasing the availability of macronutrients, but it can also lead to reduction in the availability of cationic micronutrients when applied at high rates. The aim of this study was to evaluate the effect of application of high rates of limestone, incorporated in the 0–0.40 m soil layer, on nutrient availability and their relation to cumulative grain yield in an annual crop production system. Three experiments were set up in 2017 with six liming rates (0, 3, 6, 9, 12, and 15 Mg ha−1), with incorporation in the 0–0.40 m layer. Soil and leaf samples were collected for determination of macro- and micronutrient concentration in the leaves. Regression and linear correlation analyses were used to evaluate the effect of the application rates on the availability of nutrients and on cumulative yield in soybean, maize, dry bean (common bean) wheat crops over three crop years. The micronutrient that showed the greatest reduction in level in the soil through liming was Fe, in contrast with Zn, which was not affected. The concentrations of micronutrients in soybean and common bean leaves were more sensitive to the effect of deep liming than the levels in the soil, and reductions were observed in the concentrations of B, Fe, Mn, and Zn; however, they remained at suitable levels according to regional standards. Thus, even with the reductions in the availability of the micronutrients brought about by incorporation of higher doses of limestone (≥ 9 Mg ha−1), the cumulative grain yields showed an increase in accordance with liming rates, with the optimal dosage from 8.77 to 12.6 Mg ha−1, depending on the site. The main factors that had positive correlation with yield were soil pH and the macronutrients concentration in the leaves, which generally increased along with the liming rates. • Micronutrients availability to plants reduces with increasing limestone doses incorporated at 0.40 m. • The concentrations of macronutrients in the leaves increased with increasing limestone rates incorporated at 0.40 m. • There is a positive correlation with grain yield and soil pH and macronutrient concentration in leaves. • Accumulated grain yield increases with increasing limestone rates incorporated at 0.40 m. [ABSTRACT FROM AUTHOR]