In order to evaluate the effect of biofertilizers (Rhizobium and mycorrhiza) on yield and qualitative characteristics of Pinto bean under deficit irrigation, an experiment was conducted as split plot based on a randomized complete block design with three replications in 2017. Experimental treatments included irrigation regime with two levels (normal and deficit irrigation) as main plots and biological fertilizers with six levels {Control (C), Rhizobium phaseoli (R), fungus included Rhizophagus intraradices (I) and Funneliformis mosseae (M), Integrated 1 (R. intraradices and Rhizobium-T1), Integrated 2 (F. mosseae and Rhizobium-T2)} as sub-plots. Inoculation with F. mosseae led to increase in 1000-seed weight in deficit irrigation condition. Grain yield was enhanced by 28% due to application of R. intraradices, compared with control treatment. The highest grain protein content (19.86%) was observed in Rhizobium fertilizer application under normal irrigation condition and its lowest (13.77%) was obtained from control plants under deficit irrigation condition. The maximum amount of crude protein (21.45%) and digestible dry matter (71.15%) were found in the plants treated with R. intraradices under deficit irrigation condition, and the lowest amount of them (16.72 and 58.94%) were obtained from untreated plants under normal and deficit irrigation treatments, respectively. Plants treated with F. mosseae had the highest concentrations of proline and total chlorophyll under deficit irrigation condition. Generally, F. mosseae and R. intraradices species led to improving qualitative and qualitative characteristics of Pinto bean under deficit irrigation condition.