The conservation farming systems coupled with stubble retention are now widely adopted in southern Australia to improve soil fertility. However, little information is available about the effects of winter crops on soil labile organic carbon (C) and nitrogen (N) pools, especially in an arid agricultural ecosystem. In this study, eight winter cover crop treatments were used to investigate their effects on soil labile organic C and N pools and microbial metabolic profiles and diversity in temperate Australia. These treatments included two legume crops (capello woolly pod vetch and field pea), four non-legume crops (rye, wheat, Saia oat and Indian mustard), and a mixture of rye and capello woolly pod vetch as well as a nil-crop control. At the crop flowering stage, soil and crop samples were collected from the field and we examined aboveground crop biomass, soil NH4+-N, NO3−-N, extractable organic C (EOC) and N (EON) concentrations using methods of 2M KCl and hot water, microbial biomass, biologically active organic C (CBio), and substrate-induced respiration (SIR) using the MicroResp method. Results showed that the crop treatments had lower soil moisture content, NO3−-N and the ratios of EOC to EON, but higher pH, NH4+-N, EOC, EON, CBio, microbial metabolic diversity index (H) and evenness index compared with the control. There were no significant differences in microbial biomass C and N among the treatments. Although no pronounced differences in EOC and EON concentrations were found between the legumes and non-legumes, the legume treatments had lower SIR and higher H than the non-legume treatments. Principal component analysis showed that soil microbial metabolic profiles under the crops were different from those of the control, and the crop treatments had a clear separation along principal component 2. In addition, redundancy analysis showed that soil pH and moisture content were the most important influencing factors, along with EON and crop biomass, determining the patterns of microbial metabolic profiles under the crops.