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Organic farming (OF) has been increasing in popularity over recent years, but unfortunately tends to have lower yield, due to lower nutrient availability and pest problems. To better understand how OF influences plant growth, we must elucidate the impact of such practices on the microbial community, an important factor in soil management. In this study, we examined the relationship between farming practice, changes in plant growth, and soil microbial community for green onion (Allium fistulosum L.) cultivated over 313 days in green houses with OF using composts with natural green tuff as soil conditioner (EF1) or inorganic fertilizer (EF2). Average yields of EF1 were generally higher than EF2, reaching up to 12% higher (p < 0.05; day 131). The observed soil microorganism phylotypes and phylogenetic diversity (Faith’s phylogenetic diversity (PD)) were both significantly higher (p < 0.05) in EF1 than EF2 on days 93, 191 (only for PD), and 261, based on microbial richness indices. Several phylotypes belonging to the Bacillus-related microbial order Bacillales were found at higher abundances in EF1 soils, positively correlated with specific soil properties (i.e., humus, ammonium, and pH), and may associate with plant growth promotion and/or fungal toxin degradation. These results point towards novel positive effects of OF and provide insights into the management of soil microorganisms using organic fertilizers.