Maintaining a diverse functional and taxonomic microbial community in central to preserving soil quality and for ensuring food security. Growing evidence suggests that organic farming systems possess higher quality soils with robust microbial activity in comparison to conventionally managed systems. Although plastic tunnel greenhouses are widely used, their effects on microbial communities are largely unknown. We examined how four treatments impacted soils and their microbial communities: (1) organic management in greenhouses (Or-Gr) and (2) open fields (Or-Op), and (3) conventional management in greenhouses (Co-Gr) and (4) open fields (Co-Op). We measured physicochemical and microbiological parameters, community-level physiological profiles, and phospholipid fatty acid (PLFAs) contents of soils (0–20 cm depth). Both organic and greenhouse management significantly increased total organic C (SOC), total N, microbial biomass C (MBC) and N (MBN), and basal- and substrate-induced respiration (P < 0.05). Or-Gr had significantly higher total, bacterial (both Gram-positive and -negative), and fungal PLFA concentrations (P < 0.05) than the other treatments. Generally, soil quality followed the series Or-Gr > Or-Op > Co-Gr > Co-Op. MBC, MBN, and PLFA concentrations were positively correlated (r > 0.90, P < 0.01) with SOC, total N, and cation exchange capacity and negatively with soil pH. Organic and greenhouse management had a significant interaction effect. Our findings suggest that greenhouse management should be promoted for food security.