In this study soil enzyme analysis, microbial cultivation and Biolog analysis were employed to evaluate the microbial activity and functional diversity of soil enclosed in a polythene tunnel greenhouse or “polytunnel”, intended for the cultivation of cucumbers (Cucumis sativus L.) or tomatoes (Lycopersicon esculentum Miller). The results show that the dehydrogenase activity of the soil kept in the polytunnel under recommended fertilization is 36.5% higher than that under conventional fertilization. In addition the dehydrogenase activity of the polytunnel soil used to grow tomatoes under recommended fertilizer inputs significantly increased by 66.5% when compared with conventional practices. The number of culturable actinomycetes of both cucumber and tomato soils cultivated in the polytunnels significantly increased by 30.0% and 72.2%, respectively, when compared with conventional fertilization. The Biolog analyses indicate that AWCD (Average Well Color Development) in tomato soils under recommended fertilization are always greater than those under conventional or no fertilizer treatments when incubated in polytunnels. The AWCD incubated at 96 hrs in cucumber soils and in the polytunnel under recommended fertilization were 36.5% higher than that under conventional fertilization. Similarly, in tomato soils kept in the polytunnel, the AWCD at 96 hrs under recommended fertilization had significantly increased by 68.5% when compared with conventional fertilization. The Shannon, Simpson and McIntosh indices of polytunnel greenhouse tomato soil microbial communities under recommended fertilization were higher than those under conventional fertilization. The McIntosh index was significant at p<0.05. PCA analyses suggests that carbon utilization of the soil microbial communities in the cucumber and tomato soils under recommended and conventional fertilization differ markedly from each other.