Zinc (Zn) availability is limited in salt-affected soils due to high soil pH and calcium concentrations causing Zn fixation. The application of synthetic Zn fertilizer is usually discouraged due to the high cost and low Zn use efficiency. However, salt-tolerant Zn-solubilizing bacteria (ZSB) are capable of solubilizing fixed fractions of Zn and improving fertilizer use efficiency. In the current study, a product was formulated by coating urea with bioaugmented zinc oxide (ZnO) to improve wheat productivity under a saline environment. The promising ZSB strain Bacillus sp. AZ6 was used for bioaugmentation on ZnO powder and termed as Bacillus sp. AZ6-augmented ZnO (BAZ). The experiment was conducted in pots by applying urea granules after coating with BAZ, to evaluate its effects on wheat physiology, antioxidant activity, and productivity under saline (100 mM NaCl) and non-saline (0 mM NaCl) conditions. The results revealed that the application of BAZ-coated urea alleviated salt stress through improving the seed germination, plant height, root length, photosynthetic rate, transpiration rate, stomatal conductance, soil plant analysis development (SPAD) value, number of tillers and grains, spike length, spike weight, 1000-grain weight, antioxidant activity (APX, GPX, GST, GR, CAT, and SOD), and NPK contents in the straw and grains of the wheat plants. Moreover, it also enhanced the Zn contents in the shoots and grains of wheat by up to 29.1 and 16.5%, respectively, over absolute control, under saline conditions. The relationships and variation among all the studied morpho-physio and biochemical attributes of wheat were also studied by principal component (PC) and correlation analysis. Hence, the application of such potential products may enhance nutrient availability and Zn uptake in wheat under salt stress. Therefore, the current study suggests the application of BAZ-coated urea for enhancing wheat’s physiology, antioxidant system, nutrient efficiency, and productivity effectively and economically.