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.