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Increased dependence of resource-poor rural communities on soils of low inherent fertility are the major problem of desert agroecosystem. Agrisilviculture practices may help to conserve the soil biota for maintaining essential soil properties and processes in harsh climate. Therefore, the impacts of different land use systems on faunal density, nutrient dynamics and biochemical properties of soil were studied in agrisilviculture system of Indian desert. The selected fields had trees (Zizyphus mauritiana, Prosopis cineraria, Acacia nilotica) and crops (Cuminum cyminum, Brassica nigra, Triticum aestivum) in different combinations. Populations of Acari, Myriapoda, Coleoptera, Collembola, other soil arthropods and total soil fauna showed significant changes with respect to different land use practices and tree species, indicating a strong relation between above and below ground biodiversity. The Coleoptera exhibited greatest association with all agrisilviculture fields. The Z. mauritiana system indicated highest facilitative effects (RTE value) on all groups of soil fauna. Soil temperature, moisture, organic carbon, nitrate- and ammonical-nitrogen, available phosphorus, soil respiration and dehydrogenase activity were greater under tree than that of tree plus cropping system. It showed accumulation of nitrate-nitrogen in tree field and more utilization by crops in cultivated lands. Positive and significant correlation among organic carbon, nitrate- and ammonical-nitrogen, phosphorus, soil respiration and dehydrogenase activity clearly reflects increase in soil nutrients with the increase in microbial and other biotic activity. P. cineraria field was the best pedoecosystem, while C. cyminum was the best winter crop for cultivation in desert agroforestry system for soil biological health and soil sustainability. The increase in organic carbon, soil nutrients and microbial activity is associated with the increase in soil faunal population which reflect role of soil fauna in fertility building. This suggests that strategies may be developed for nurturing fertility-building soil fauna and managing degraded pedoecosystem in desert just by adopting suitable agricultural practices.