Soil microbes and protozoa, as important members of soil biota, play key roles in soil ecological processes due to their abundances and communities closely associated with various agricultural activities. In this paper, a comparative study was conducted to study the effects of organic (ORG), low input (LOW), and conventional (CON) vegetable greenhouse systems on soil microbial biomass carbon (bacterial and fungal biomass carbon) and protozoa abundance. Soil samples were collected five times from August to December 2012 (an entire cucumber growing season) in the Quzhou Experimental Station of China Agricultural University. The results showed that the management practices significantly affected soil fungal biomass carbon, bacterial biomass carbon, microbial biomass carbon, flagellate abundance, ciliate abundance, amoeba abundance and total protozoa abundance, but did not affect the fungal to bacterial (FB) ratio and the relative abundances of flagellates and amoebae. Generally, soil bacterial, fungal, and microbial biomass carbon values were in an order of ORG > LOW > CON, and this trend was more obvious in 0-10 cm soil. FB ratio indicated a bacterial-based decomposition pathway in all three systems, which exhibited similar dynamic characteristics. For protozoa, flagellates dominated under all three management practices, with a mean proportion of 85.2%, followed by amoebae (13.1%), and ciliates (1.7%). The total protozoa under ORG management practice were higher than those under LOW and CON management practices. In conclusion, management practice mainly affects the biomass of microbes and protozoa, whereas little effect on the functional group structure of soil biota.