Establishing highly productive forest plantations or crops on poor soils requires appropriate management to ensure sustainable production. The current development of various ecological intensification practices calls for efficient tools to monitor their effects on agro-ecosystems. Ecological intensification such as an association between a N2-fixing tree species and a highly productive species, e.g. an acacia and a eucalypt, is an agro-ecological plantation design that can enhance nutrient cycling and preserve soil fertility in tropical and sub-tropical areas. In this study, Anionic Exchange Membranes (AEM) were used to assess in situ the effect of tree species on the availability and spatial variability of nitrate (N) and phosphorus (P) in pure Acacia mangium (A), pure eucalypt (E) and mixed-species treatments (MA-ME) in a randomized complete block design on a ferralitic arenosol. The results showed that the AEM detected the specific influence of tree species on N and P availability at the stand level as well as interactions between trees in the mixed-species treatment. Moreover, nutrients trapped using AEM were significantly correlated with N and P immobilized in the tree biomass. In the mixed stand, AEM made it possible to understand the specific impact of each tree species on N and P availability reflecting the respective biogeochemical mechanisms at work. This preliminary study showed that AEM are a promising tool that can be used in situ for intensive sampling in multi-local comparisons to highlight the effect of management practices on soil fertility as well as the relationships between vegetation cover and soil.