Fruit orchards are vital in delivering both economic and environmental services, yet their potential for carbon sequestration remains underexplored. Estimating carbon sequestration is important in semi-arid regions where vegetation cover is sparse; the perennial biomass adds litter inputs that enhance soil carbon storage and improve soil fertility. Quantifying carbon sequestration provides valuable insights into the role of fruit-based orchards in climate change mitigation in fragile ecosystems, thereby contributing to sustainable ecosystem services. The present investigation was carried out in different fruit orchards, viz. Ficus carica, Cordia myxa, Citrus limon, Citrus jambhiri and Aegle marmelos at ICAR-Central Arid Zone Research Institute, Regional Research Station, Pali Marwar, Rajasthan, India. Since fruit is an economic part, a non-destructive method based on tree dimensions (tree height and diameter) was used for biomass and carbon estimation. The results revealed significant differences among different species of fruit orchard (p < 0.001). C. myxa (29.28 ± 14.18) and A. marmelos (27.04 ± 9.60) recorded total carbon stock (kg tree-1) on par with each other. Pearson correlation coefficient indicates that tree height is positively correlated with above-ground biomass (AGB) and carbon stock (0.98). Among the five fruit orchards, Soil organic carbon (SOC) was highest in C. myxa irrespective of depth (8.45 Mg ha-1). C. myxa and A. marmelos are indigenous fruit tree species that can serve as potential carbon sinks and may be promoted for farmer adoption through supportive policies in the arid and semi-arid regions of Rajasthan.