Soils in the high jungle region of Peru continuously face erosion due to heavy rain, which leads to significant nutrient losses. Leguminous plants may provide a sustainable solution to this problem due to their ability to fix atmospheric nitrogen with the help of symbiotic rhizospheric microbes that reside in their root nodules and help restore soil fertility. The aim of this study was to isolate native rhizobial strains that can form functional nodules in red kidney beans to help improve their growth, development, and yield in field conditions. Rhizobium strains were isolated from soil samples collected from coffee fields using bean plants as trap hosts. The strain RZC12 was selected because it showed good root nodule promotion and a number of PGPR (plant-growth-promoting rhizobacteria) attributes. In the field, bean plants inoculated with the strain RZC12 and co-cultivated with coffee plants produced approximately 21 nodules per plant, whereas control plants produced an average of 1 nodule each. The inoculation with RZC12 significantly increased plant length (72.7%), number of leaves (58.8%), fresh shoot weight (85.5%), dry shoot weight (78%), fresh root weight (85.7%), and dry root weight (82.5%), compared with the control. The dry pod weight produced by the plants inoculated with RZC12 was 3.8 g, whereas the control plants produced 2.36 g of pods. In conclusion, RZC12 is a promising strain that can be used in field conditions to improve the overall productivity of red kidney beans.