Although an increasing number of analytical techniques and methods are becoming available for the detection, identification and quantification of nanoparticles (NPs) during the nanomaterial production process, their application is still a major challenge due to the complex composition of nanomaterials. Here we develop a new comprehensive set of fit-for-purpose analytical tools for characterisation of NPs, thus enabling a fundamental understanding of their structure, further alteration, and chemical functionalization during the production process. Specific study cases will be (1) bimetallic nanoparticles used as catalysts for development of sustainable methods for synthesis of bio-based chemicals, (2) glycan-functionalised gold nanorods, and (3) iron oxide-core NPs with a Au mono-layer, functionalized with an antibody, both used for medical purposes. The innovative aspect of our study lies in the multidisciplinary and complementary analytical approach. This will lead to a set of sufficiently precise, accurate and robust techniques for comprehensive characterization of the functionalized NPs by (i) optimisation of existing analytical techniques/instrumentation, and more importantly, (ii) development of new analytical tools and methods, (iii) implementation of new coupling techniques for improved hyphenation, and (iv) novel sample introduction systems.