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Thirty‐five bacterial isolates, recovered from the healthy bulbs of Allium sativum that grow in different sites of China, were screened for their ability to produce hydrolytic enzymes and metabolites and to dissolve inorganic phosphorus in vitro. These 35 endophytes inhibited the growth of the causal agent of white rot disease, Sclerotium cepivorum (Sc), by 19–64%. The isolates 153 (Bacillus siamensis) (Bs) and 136 (Streptomyces setonii) (Ss) were found to be the most effective in decreasing Sc disease incidence, both by 66%. In addition, there was a significant enhancement in the growth of garlic plants pretreated with isolates 153 Bs and 136 Ss. Isolate 136 could not produce indole‐3‐acetic acid (IAA) and did not exhibit an inorganic phosphorus solubilization ability in vitro. Thus, growth promotion by this Streptomyces sp. is likely to be mediated by a different, and perhaps novel, mechanism to that typically associated with growth promoting bacteria. An increase in expression of alliin lyase 2 was found in garlic plants treated with 153 Bs. By extension, the quantity of the antimicrobial sulphoxide, alliin, was also increased in 153 Bs‐treated and Sc‐inoculated plants, relative to the Sc‐inoculated controls. These results indicated that this bacterial endophyte might protect A. sativum not only by direct antibiosis, but also by enhancing the expression of alliin lyase 2 and the concomitant production of alliin.