Nanotechnology is the new industrial revolution of our century. Its development leads to an increasing use of nanoparticles and thus to their dissemination. Their fate in the environment is of great concern and especially their possible transfer in trophic chains might be an issue for food safety. However, so far our knowledge on this topic has been restricted by the lack of appropriate techniques to characterize their behavior in complex matrices. Here, we present in detail the use of cutting-edge beam-based techniques for nanoparticle in situ localization, quantification and speciation in a crop plant species (Lactuca sativa). Lettuce seedlings have been exposed to TiO2 and Ag nanoparticles and analyzed by inductively coupled plasma spectrometry, micro-particle induced X-ray emission coupled to Rutherford backscattering spectroscopy on nuclear microprobe, micro-X-ray fluorescence spectroscopy and X-ray absorption near edge structure spectroscopy. The benefits and drawbacks of each technique are discussed, and the types of information that can be drawn, for example on the translocation to edible parts, change of speciation within the plant, detoxification mechanisms, or impact on the plant ionome, are highlighted. Such type of coupled approach would be an asset for nanoparticle risk assessment.