Literature suggests that terrestrial plants can internalize and translocate nanoparticles mainly via apoplastic transport. Direct evidence for the mechanisms driving the NP uptake and their mobility in plants, especially for non-dissolving metal-based NPs, is currently scarce at the cellular level. Here, the NP-root interactions of negatively and positively charged gold NPs ((-/+)Au-NPs) were investigated in Arabidopsis thaliana using complementary tools: -X-ray fluorescence (-XRF), computed nanotomography (nano-CT), and dark-field microscopy combined with hyperspectral imaging (DF-HSI). These developed, tested and cross-validated tools improve our ability to track and semiquantitatively analyze environmentally relevant NP concentrations in complex media. Nano-CT displays a three-dimensional volume with a detection limit of less than tens of Au-NPs/voxel for~12 nm diameter Au-NP (equivalent to ~1.7 g.(+)Au.kg-1 , fresh plant tissue). Results also provide direct evidence that shoved-off detached border cells associated mucilage accumulate and trap large amounts of both (-/+)Au-NPs. Contrariwise, border cells attached to the root behaved charge-specific and seems to influence Au-NP uptake: (+)Au-NPs adsorbed onto mucilage, which prevented uptake into the root tissue. Negatively charged (-)Au-NPs did not adsorb to mucilage, and were shown to translocate into the apoplast to a small extent.