In the Vakinankaratra region of the Malagasy Highlands, rainfed rice cultivation has developed rapidly, which has led to rapid degradation of soil fertility and reduced productivity. This study involved a comparison of rainfed rice in rotation with maize/Brachiaria (MZ-BR) or maize/soybean (MZ-SB) intercrops, managed by direct seeding (DS) or plowed with residue burial (PB) with conventional mineral fertilization (FM) or without fertilizer (F0). The umbric Acrisol (hyperdystric) presented an anion exchange capacity (AEC) and variable charge according to the pH. Mineralizable nitrogen (Nminz.) values decreased sharply from the surface to the deep horizons and became almost nil in the 90–120 cm horizon, while the Nminz. contents of the DS treatments were systematically 5–7% higher than the PB treatment values for a given depth. The AEC of the 0–10 cm horizon was practically zero but increased significantly with depth and reached 2.58 cmol(c) kg-1. AEC values were inversely correlated with the organic carbon (Corg.) content: AEC = 1.81–0.375 Corg. The nitrate adsorption isotherms were linear and the nitrate partition coefficients (coef_nit) were correlated with the AEC values: coef_nit = 0.3363 AEC+0.1855 (R2 = 0.954). The soil nitrate stock determinants were highlighted by the matrix of correlations of the principal component analysis: excheangeable acidity and aluminum, cation exchange capacity, ¿pH, Corg. and clay and total silt contents were particularly important for the AEC and coef_nit. The different cropping systems showed no significant impact after 12 years on soil characteristics that could improve nitrogen bioavailability. We thus recommend using organic fertilization to raise the soil pH, Corg. content and nitrogen bioavailability.