Chickpea is mostly grown in sandy loam soils having receding soil moisture and Zn deficiency, which limits the chickpea productivity. Zn solubilizing plant growth-promoting bacteria (PGPB) may improve the availability and uptake of Zn in these soils. This 2-year field study was conducted to evaluate the interactive effects of pre-optimized Zn application methods and Zn solubilizing PGPB (i.e., endophyte Enterobacter sp. MN17) on the productivity and quality of desi chickpea during 2016–2017 and 2017–2018. Zn was delivered through osmopriming (0.001 M Zn solution), seed coating (5 mg Zn kg−1 seed), foliar application (0.025 M Zn solution), and soil application (10 kg Zn ha−1) with or without Zn solubilizing PGPB, while hydroprimed seeds were taken as control. Zn application through either method improved the grain yield, economics, bioavailable Zn, and grain quality of desi chickpea. The maximum improvement in grain yield (43.7%) was recorded with Zn soil application followed by Zn seed coating (38.8%). The highest protein contents (22.8%), grain Zn concentration (45.8 μg g−1), bioavailable Zn contents (4.38 mg Zn day−1), and minimum phytate contents (12.0 mg g−1) were recorded by Zn soil application. The maximum mineral matter (3.89%) and fiber contents (4.81%) were recorded with Zn soil application + PGPB. The maximum agronomic efficiency (6409 kg kg−1), agro-physiological efficiency (160 kg kg−1), and apparent recovery efficiency (76.8%) were noted by Zn osmopriming + PGPB. However, the maximum physiological (289 kg kg−1) and utilization (10,559 kg kg−1) efficiencies were recorded with Zn osmopriming. Moreover, the highest economic returns ($1518.2 ha−1) and marginal net benefits ($571.5 ha−1) were recorded with Zn soil application + PGPB. To improve the productivity, profitability, and grain quality of desi chickpea, Zn application through soil or seed coating in combination with plant growth-promoting bacteria may be opted to maximize the productivity and profitability.