<p>Maize is highly responsive to nitrogen, but its use efficiency declines under water stress and high temperatures—common in rainfed soybean–maize systems in tropical regions with two crops per year. Surface-applied urea at the V4 stage often performs poorly due to limited post-application rainfall. This study aimed to compare the efficiency of surface-applied conventional nitrogen (N)-fertilizer with enhanced-efficiency sources placed in the maize sowing furrow. To improve operational efficiency during sowing, we also evaluated system phosphorus (P)-fertilization—applying the full P requirement of both crops to a single crop—on soils with built-up P fertility. This strategy was compared with conventional fertilization, where each crop receives phosphorus separately in the sowing furrow. A randomized complete block design with a split-split plot arrangement was used, with locations as the main plot, P-fertilization methods as subplots, and N-sources and application methods as split-split plots. Evaluated variables included nutrient concentrations in leaves, grain yield, plant and ear height, chlorophyll index, and maize ear traits such as rows and grains per row. Soybean yield was unaffected by P-fertilization method, but maize yield declined without furrow-applied P. Enhanced-efficiency N-fertilizers applied in the furrow improved chlorophyll index and maize yield compared to conventional nitrogen sources. In rainfed soybean–maize systems on clay soils with built-up phosphorus fertility, system phosphorus fertilization—by applying the full phosphorus dose to maize—can be adopted without yield losses in either crop. Additionally, enhanced-efficiency nitrogen fertilizers proved more effective than urea in supplying nitrogen to maize.</p>