Chickpeas are rich source of protein and predominantly grown in boron (B)-deficient sandy-loam soils in Pakistan. Boron-tolerant bacteria (BTB) could tolerate higher B levels in soil and increase B availability to the plants. Field trials were conducted under irrigated (district Layyah) and rainfed (district Chakwal) conditions to evaluate the interactive effects of pre-optimized B application methods and BTB (Bacillus sp. MN54) on the nodule’s population, grain quality, productivity, and grain-B concentration in desi chickpea during 2019–2020 and 2020–2021. Boron was applied as soil application (1 kg B ha−1), foliar application (0.025% B), osmopriming (0.001% B), and seed coating (1.5 g B kg−1 seed) with or without BTB inoculation. Untreated seeds receiving no B through any of the methods were regarded as control. The individual and interactive effects (up to three-way interaction of location × BTB inoculation × B application methods) of year, location, B application methods and BTB inoculation significantly altered the growth and yield-related traits of desi chickpea. The four-way interaction of year × location × BTB inoculation × B application methods was non-significant for all recorded growth and yield-related traits. Regarding individual effects, the higher values of growth and yield-related traits were noted for 2020–2021, rainfed location, BTB inoculation and B application through seed priming. Similarly, in two-way interactions 2020–2021 with rainfed location and BTB inoculation, rainfed location with BTB inoculation and osmopriming and osmopriming with BTB inoculation recorded higher values of the growth and yield-related traits. Osmopriming combined with BTB inoculation significantly improved dry matter accumulation and leaf area index in both locations. Boron application through all the methods significantly improved grain quality, yield grain B concentration. The highest grain and biological yields, and nodules’ population were recorded with osmopriming followed by soil application of B combined with BTB inoculation. The highest plant B concentration (75.05%) was recorded with foliar application of B followed by osmopriming (68.73%) combined with BTB inoculation. Moreover, the highest economic returns (USD 2068.5 ha−1) and benefit–cost ratio (3.7%) were recorded with osmopriming + BTB inoculation in 2020–2021 under rainfed conditions. Overall, B application through osmopriming and soil application combined with BTB inoculation could be used to increase productivity and profitability of desi chickpea, whereas foliar application is a better method to enhance grain and plant B concentration.