Conservation agriculture commonly improves soil health and results in organic C sequestration. This study compared conventional tillage (CT) and no tillage (NT) systems, examining differences in stubble management [stubble burning (SB) and stubble retention (SR)] and N fertilization on soil C, C fractions and N. The experiment was established in 1968 on a Vertisol at Hermitage in Queensland, Australia. After 50 years of management; it was found that the tillage regime, the addition of N fertilizers, and the stubble management were all important in influencing soil C pools in 0-0.1 m of soil depth. Overall, the addition of N fertilizers and the tillage regime were the most important management factors. For example, the addition of N fertilizers at a rate of 90 kg ha(-1) resulted in an average increase in SOC of 18%, while use of NT resulted in an average increase in SOC of 5%. Similarly, application of N fertilizers increased total soil N (TSN) concentrations <= 25.5%, increased the stabilized SOC fraction by <= 26.6%, and increased microbial biomass C by <= 22%. Regardless, stubble management practices were also important, with the retention of stubble increasing TSN, increasing the stabilized C fraction, and increasing the microbial biomass C <= 30%. Finally, it was observed that the microbial metabolic quotient was 39% higher when stubble was burned and in the absence of N fertilization, indicating microbial stress under these treatments. The study clearly shows the importance of stubble retention and N fertilization in conservation agriculture for improvement in soil health and maintenance of soil C levels.