In tropical conservation agricultural systems, crop yield is limited by soil acidity and root-growth inhibition, especially under intensive crop rotation. This study evaluated the effect of surface applications of lime and phosphogypsum in improving soil fertility and crop yield in a tropical region. Four treatments were evaluated: control (without soil amendment); and application phosphogypsum (2.1 + 2.1 + 2.1 Mg ha^–1), lime (2.7 + 2.0 + 2.0 Mg ha^–1), and a combination of lime and phosphogypsum at the given rates, applied in 2002, 2004 and 2010, respectively. We evaluated the soil chemical properties, root development, plant nutrition, yield components and grain yield of 10 crops over 4 years using five species: maize (Zea mays), crambe (Crambe abyssinica), cowpea (Vigna unguiculata), wheat (Triticum aestivum) and common bean (Phaseolus vulgaris). Our long-term results demonstrate the benefits of surface liming in alleviating subsoil acidity, reducing Al³⁺ toxicity, improving availability of Ca²⁺ and Mg²⁺, and increasing accumulation of soil organic matter in all soil profiles at depths up to 0.60 m. For maize and crambe, adding phosphogypsum increased development of plants and reproductive structures, which increased grain yield. Phosphogypsum exhibited synergistic effects in association with lime for maize and common bean. Phosphogypsum did not have an effect on cowpea and wheat, whereas surface liming was essential to improve plant nutrition, grain yield and wheat grain quality. The combination of both soil amendments is an important tool to reduce the soil acidification process, resulting in the highest levels of Ca²⁺ and Mg²⁺ and the highest base-saturation values in the topsoil layers (0–0.20 m) over time. Our long-term results showed the viability of surface liming plus phosphogypsum for improving tropical soil fertility, which can reflect an increase in grain yield and contribute to the sustainability of agricultural systems under intensive land use in highly weathered areas.