The study aims at determining the effect of the treatment method of root crops before storage, as well as storage parameters, on the dynamics of their microflora, namely, the quantity of bacterial microflora, mesophilic aerobic and optionally anaerobic microorganisms (MAaOAM), as well as molds. When storing garden carrot at t = +(2±1) °C (during 56 days), the amount of bacterial microflora of the samples subjected to integrated treatment decreased by 2.5 times by the end of storage; the number of mold fungi decreased twice compared to the control. When storing garden carrot at t = +(25±1) °C (for 21 days) the amount of bacterial microflora in the samples treated by electromagnetic fields of extremely low frequencies (with the following parameters: frequency – 28 Hz, the treatment time – 5 min, the magnetic induction – 12 mTl), and by Vitaplan biologic preparation (at the concentration of 106 CFU/g, and in the amount of 2.5 ml/kg), decreased by 2.1 times, while the number of mold fungi reduced by 1.5 times. When storing garden beet at t = +(2±1) °C for 56 days, the amount of bacterial microflora of samples, subjected to integrated treatment for 5 min at a frequency of 15, 24, and 30 Hz, and magnetic induction of 9 mTl, as well as treatment with Bactofit biological preparation (at the concentration of 106 CFU/g in amount of 2.5 ml/kg), decreased by 1.5 times compared to the control, while the number of mold fungi decreased by 2.3 times. When storing garden beet at t = +(25±1) °C (for 21 days), the quantity of bacterial microflora of samples, subjected to integrated treatment, was by 2.8 times lower compared to the control, while the number of mold fungi reduced by 1.8 times. It has been revealed that the integrated treatment of root crops with biopreparations and extremely low frequency (ELF) electric and magnetic fields (EMF) more effectively inhibits the development of pathogenic microflora compared to treatment only with biopreparations or treatment only by ELF-EMF. Significant retardation of growth rates was revealed in both bacterial and fungal pathogenic microflora during storage of root crops at different temperatures.