Environmental crises, land degradation, and frequent crop failure threaten the livelihoods of millions of the populace in the semi-arid agroecosystems. Therefore, different combinations of annual crops with perennial fruit trees were assessed to restore the soil carbon, and enhance farm productivity and profitability in a semi-arid climate. The study hypothesized that the integration of perennial fruit trees with seasonal crops may enhance farm productivity, economic returns, and environmental sustainability. Integration of phalsa ( Grewia asiatica) with mung bean ( Vigna radiata) - potato ( Solanum tuberosum) system recorded the highest system productivity (25.9 Mg/ha) followed by phalsa with cowpea ( Vigna unguiculata) -mustard ( Brassica juncea) systems (21.2 Mg/ha). However, Karonda ( Carissa sp.) with mung bean - potato system recorded maximum net return (3529.1 US$/ha), and water use efficiency (33.0 kg/ha-mm). Concerning the benefit-cost (B:C) ratio, among the agroforestry systems, the karonda + cowpea - mustard system registered a maximum BC ratio (3.85). However, SOC density remained higher (9.10 Mg/ha) under the phalsa + cowpea - mustard and Moringa + mung bean - potato system (9.16 Mg/ha) over other systems. Similarly, phalsa + mung bean - potato system had the highest C sustainability index (27.6), carbon sequestration potential (0.6–0.67 Mg/ha/year), and water use efficiency (33.0 kg/ha-mm). Hence, the study suggested that the integration of short-duration leguminous and oilseeds with fruit trees offer a myriad of benefits and an efficient system for restoring the soil C without compromising the food and livelihood security of the rural populace in semiarid regions.