Conservation agriculture (CA) is one strategy with which both sustainability and productivity can be achieved by improving soil health. However, linkages between practices, soil health and cropping system performance remain poorly disentangled. We assessed the relationships between soil health and cropping system performance for three maize-based cropping systems in New Caledonia. Two CA systems, one with direct seeding into a mixed species dead mulch (CA-DM) and one into a stylo living mulch (CA-LM), were compared to a conventional tillage (CT) system. CA vs. CT experiment started in 2011, whereas the differentiation between CA-DM and CA-LM was initiated in 2017 only. In 2018, soil health was evaluated using Biofunctool (R), a set of ten in-field tools that assess soil carbon transformation, structure maintenance and nutrient cycling functions. The performance of the three cropping systems were assessed by monitoring weeds, maize growth and yield components. Structural equation modelling (SEM) was used to disentangle the links between agricultural management, soil health and cropping system performance. Soil structure maintenance and nutrient cycling functions were higher under CA-DM and CA-LM than under CT, and carbon transformation function was higher under CA-DM than under CT and CA-LM. Overall, the soil health index (SHI) was 1.3-fold higher under CA systems than under CT. Cropping system management had both direct and indirect effects on soil functioning and crop productivity leading to a 1.3-fold higher yield under CA than under CT. The direct and indirect effects of CA systems on soil health had positive impacts on ecosystem services (i.e., productivity, weed regulation and soil ecosystem services). Such integrative approaches that account for the relationships and possible trade-offs between cropping system components enable a better understanding of the effects and the performance of practices, and support adaptive agricultural management.