A field experiment was conducted during 2022–23 to 2024–25 at the AICRPDA Research Farm, Tamil Nadu Agricultural University, Kovilpatti, India, to evaluate climate-smart agri-horti systems integrating aonla (Phyllanthus emblica Gaertn.) and custard apple (Annona squamosa L.) with annual intercrops under rainfed conditions. The experiment, laid out in a split-plot design with three replications, included fruit tree species as main plots and blackgram (Vigna mungo L.), greengram (Vigna radiata L.), clusterbean (Cyamopsis tetragonoloba L.), and foxtail millet (Setaria italica L.) as sub-plot treatments. Custard apple–based systems consistently produced higher fruit yield (2674–3306 kg ha⁻¹), intercrop biomass, and blackgram equivalent yield (1337–1653 kg ha⁻¹) than aonla-based systems (1980–2538 kg ha⁻¹ of fruit yield), and 891–1142 kg ha⁻¹ of blackgram equivalent yield of intercrops, respectively), primarily due to improved light availability and favourable canopy architecture. Clusterbean and foxtail millet recorded the highest intercrop yields, whereas pulse intercrops enhanced tree growth, soil nitrogen availability, and system sustainability through biological nitrogen fixation. Maximum rainwater use efficiency and land equivalent ratio were achieved under custard apple + clusterbean and aonla + foxtail millet combinations, indicating superior resource-use efficiency. Relative economic efficiency peaked in aonla + foxtail millet (341.2%), while the highest system profitability was recorded in custard apple + foxtail millet (₹352.4 ha⁻¹ day⁻¹). Soil fertility improved significantly over the study period, with increases in soil organic carbon (1.05–1.76 g kg⁻¹), available nitrogen (9–11 kg ha⁻¹), and potassium (8–14 kg ha⁻¹), particularly under pulse-based systems, whereas available phosphorus in soil remained unchanged. The study demonstrates that integrating short-duration legumes and millets with perennial fruit trees enhances productivity, profitability, rainwater-use efficiency, and soil health, providing a resilient and sustainable strategy for intensifying rainfed agroecosystems.