As a response to the worldwide challenge raised by soil degradation, Conservation Agriculture (CA) was proposed to help restoring the three main soil functions, i.e. carbon transformation, nutrient cycling and structure maintenance. However, there is still a lack of integrative studies that assess the overall impact of CA on soil health. To fill the gap, Biofunctool®, a set of in-field indicators, was developed to monitor changes in soil biological functioning. In this study, Biofunctool® was used to assess the impact of a conventional tillage (CT) and three CA annual-based cropping systems on soil health on a Cambodian Oxisol. Eight indicators related to the three soil functions were monitored and integrated into a Soil Quality index (SQI), i.e. the Biofunctool® Index. Overall, we found that soil health was twice higher under the CA treatments than under CT treatment. Although it was similar in the three CA treatments, the contribution of each soil function to the soil health diverged. An analysis of soil carbon dynamics also showed that CA support short-term soil organic carbon stabilization compared to CT. This study demonstrates that Biofunctool® is a robust, relevant, time-and cost-effective in-field assessment tool that can be used in multiple ways including cropping system management, capacity building of local stakeholders, and policy dialogue.