Despite numerous positive effects on the environment, increased demands, intense research, and adequate public attention, crops grown according to the principles of organic production still occupy considerably small areas. It is difficult for certified producers to decide to expand the production of certified organic vegetables. One of the reasons is the insufficiently developed growing technology of different vegetable species in accordance with the law and regulations on organic production. Intercropping, growing of subsequent crops, and application of microbiological fertilizers are considered as the most useful techniques for yield increases in sustainable growing practices. The aim of this study was to investigate the possibilities for enhancing root yield of beetroot and radish, when grown as second crops in an organic double-cropping production system. The effects of intercropping and applying microbial fertilizers on the vegetable root weights were assessed. Intercropping was with green beans, implemented by replacement series method. Two microbial fertilizers were applied, one containing selected strains of Bacillus megatherium, B. licheniformis, B. suptilis, Azotobacter chrocoocum, A. vinelandi and Derxia sp. (M1), and other with Bacillus subtilis, Azotobacter sp., Penicillium oxalicum and Fusarium sp. (M2). Intercropping and microbial fertilizers contributed to the root weight increase. The highest root weights were noted for the intercropped plants treated with M1 (beetroot, 151.8 g) and M2 (radish, 351.0 g), which was 23.5% and 15.5% higher than in the sole crop unfertilized control. The results imply combining intercropping and the appropriate microbial fertilizers as an effective strategy for increasing yields of organically grown beetroot and radish.