AbstractWhile it is acknowledged that invasive species are a global driver of land degradation, their effects are often only noticed when the invasion has been going on for a while. However, early stage processes must play a fundamental role in plant establishment until invasive plants are able to outgrow the native vegetation. In ten plots of 100 m2 each, we tested the hypothesis that belowground properties are associated with early invasion processes aboveground. We examined the early stage of invasion by a woody legume (Acacia longifolia), growing in the canopy of native dune shrubs (Corema album) as a model system in oligotrophic primary dunes in southern Portugal. Biomass under canopies of invaded and non‐invaded C. album shrubs as well as organic matter (OM) distribution in various soil fractions was measured. In accordance with our hypothesis, A. longifolia presence was related to increased C. album foliar δ15N, a proxy for nitrogen derived from the invasive legume. Under invaded canopies, root and rhizosphere biomass were higher, as was OM in the silt‐clay fraction. Also, δ15N of the OM in the silt‐clay fraction under invaded canopies was enriched, while δ13C was depleted. Finally, we found that the ratio between OM in the biotic versus soil compartment could be a good early indicator for invasion. These findings suggest that even when aboveground invasion pressure on the system is low, it is imperative for ecosystem conservation to remove young plants, as they might alter soil functioning already at an early stage of invasion. Copyright © 2017 John Wiley & Sons, Ltd.