Watering is known to convert deserts into oases. However, information on how irrigation brings changes in physical and chemical properties of soils in a desert biome is not yet known, though pertinent to land use planning. This study reports influence of irrigation and cropping sequence on physico-chemical properties of soils in the Thar Desert, Rajasthan, India. Treatments included three irrigation conditions (not irrigated, low-irrigated, and high-irrigated) and eleven cropping sequences, cotton-gram (C-G), mung bean-mustard (M-Mu), moth bean-wheat (Mo-W), moth bean-mustard (Mo-Mu), cotton-fallow (C-F), cotton-wheat (C-W), cotton-mustard (C-Mu), mung bean-wheat (M-W), moth bean-fallow (Mo-F), mung bean-fallow (M-F), and pearl millet-fallow (P-F). The irrigation reduced soil temperature (9.7 to 12.2%) and bulk density (5.3 to 6.6%), but increased silt (5.1 to 7.2%) and clay (3.8 to 5.4%) content, water holding capacity (50 to 58.3%), moisture content at field capacity (100 to 133.3%), concentration (2.3 to 3.1 times), and stock (2.2 to 3.0 times) of soil organic carbon (SOC), microbial biomass carbon (4 to 8 times), available phosphorus (1.82 to 2.1 times), and potassium (25.9 to 67.1%). These changes were higher in the high-irrigated than the low-irrigated conditions. Cropping sequences C-W, C-Mu, and C-G sequestered more SOC and retained higher microbial biomass carbon, whereas M-Mu, Mo-W, Mo-Mu and M-W maintained the highest level of phosphorus and potassium. These observations suggest that irrigation and cropping sequence are promising management options for enhancing carbon sequestration in soils, which may reduce desertification in the Thar Desert and other similar deserts in the hot tropics.