This paper addresses a new non-destructive testing (NDT) system composed by a planar eddy currents (EC) probe (ionic probe), electronic devices for signal generation, conditioning and conversion, automated mechanised scanning, and analysis software. The ionic probe allows a 3D-induced current in the material and an easy interpretation of the signal based on a comprehensible perturbation of the signal. This provides enhanced lift-off immunity and improved sensitivity. The ionic system was developed focussing micro-defects detection on aluminium alloys processed by FSW. The experimental results in AA2024 welded by FSW clearly show that this system is able to detect imperfections around 50 µm, which contribute to increasing the reliability on NDT of micro-imperfections. EC conventional probes are also applied as material characterisation technique. Results are compared to micro-structural analysis, and hardness measurements show that EC can map the different zones, providing a deeper understanding on precipitate dispersion and grain shape and size.