The present study demonstrates the interactions of fungicide-tolerant symbiotic bacteria Mesorhizobium ciceri with Cicer arietinum-kitazin (KITZ) in greenhouse conditions. Under both in vitro and soil systems, KITZ imparted deleterious impacts on plants as a function of dose. The three-time KITZ dose detrimentally and maximally reduced germination efficiency, vigor index, dry matter production, symbiosis, leaf pigments and seed attributes of C. arietinum. KITZ- induced morphological alterations in root tips, oxidative damage and cell death in root cells of C. arietinum were shown by SEM. M. ciceri tolerated up to 2400 µgmL− 1 of KITZ, synthesized considerable amounts of bioactive molecules including indole-3-acetic-acid (IAA), 1-aminocyclopropane 1-carboxylate (ACC) deaminase, siderophores, exopolysaccharides (EPS), HCN and ammonia, and solubilised inorganic phosphate even in fungicide-stressed media. Following application to soil, M. ciceri improved performance of C. arietinum and enhanced dry biomass production, yield, symbiosis and leaf pigments even in a fungicide-polluted environment. At 92 µgKITZkg− 1 soil, M. ciceri maximally and significantly (p ≤ 0.05) augmented whole plant length by 41%, total dry biomass by 18%, carotenoid content by 9%, LHb content by 21%, root N by 9%, shoot P by 11% and pod yield by 15%. Additionally, M. ciceri was associated with decreased levels of stressor molecules (proline and MDA) and antioxidant defence enzymes (APX, GPX, CAT and POD) of C. arietinum plants when inoculated in soil. The symbiotic strain effectively colonized the plant rhizosphere/rhizoplane. In pesticide- contaminated soils, inoculation of M. ciceri may serve as an excellent strategy for augmenting C. arietinum productivity.