Shallot is one of the important horticultural commodities in Indonesia. Besides having many benefits, the shallot is also the main ingredient in various traditional dishes in Indonesia. A significant increase in healthy shallot production is needed to meet the increasing demand every year. The aim of this study was to obtain the best strain of endophytic bacteria and inoculation time for increasing shallot vigour through in vitro. This study used a factorial completely randomized design with two factors, the type of bacteria and the time of inoculation which was divided into 3 stages. The first stage consisted of three collections of bacteria (GO53, IB15, S12) with 12 and 24 hours of inoculation. The second stage consisted of two collections bacteria (GO53, IB15) with 4 and 6 hours of inoculation. The third stage consisted of one collection bacteria (GO53) and 4 bacterial strains isolated from shallot (T4(2), T5, T8(1), T8(2)) with 2 and 4 hours of inoculation. The results showed GO53 and T4(2) with 2 hours of inoculation were the best types of endophytic bacteria to increase vigour. The explants in this treatment survived the longest, had more shoots and leaves than the control, and induced root formation more quickly.