The combination of high aluminium (Al) saturation and severe phosphorus (P) deficiency in sub-surface soil in no-tillage (NT) systems is an obstacle hampering crop yields in Brazil. The introduction of NT without proper soil chemical correction affects crop yields in several parts of the country. The aim of this study was to evaluate the changes in soil chemical properties and response of crops to different application methods of lime and phosphate fertiliser in an Ultisol under NT. The field experiment consisted of combining surface and incorporated liming and P application (without P, surface P and P in the sowing line), plus a treatment with incorporated lime and P. The correction of soil acidity and availability of P at depth was effective with the incorporation of lime and phosphate fertiliser. Five months after lime incorporation, it was possible to increase soybean productivity by more than 40% (from 3.9 to 5.6 Mg ha−1). The surface application of P and limestone restricts the correction of soil fertility only in the uppermost soil layer evaluated (up to 5 cm). The relationship between soybean yield and soil chemical properties in different layers clearly demonstrates that neither the 0–10 cm soil layer nor the 0–20 cm soil layer is suitable for diagnosing soil fertility and the crop productive potential in NT system with chemical restrictions in subsurface. Further studies are need to establish critical levels of available P and Al saturation for subsurface soil layers in different soil types under no-tillage.