Nanoparticulate drug delivery systems (NDDSs) offer a revolutionary strategy to fighting ailments. The NDDSs are uniquely and deliberately constructed as vessels for the transport of active pharmaceutical components (APIs), which leverages their distinct physicochemical traits, such as lengthened circulation period, enhanced targeting capability and evasion of drug resistance. Although the last three decades have seen considerable progress, our comprehension of how NDDSs' pharmacokinetics in vivo can affect their safety profiles is still insufficient. Examining NDDSs is way more complex than analyzing small molecules since their structure and composition are completely different, almost making regular analytical techniques inadequate for measuring correctly its behavior within living systems. The following advanced bioanalysis techniques are summarized to trace the in vivo fate of NDDSs: liquid chromatography tandem mass spectrometry (LC-MS/MS), enzyme-linked immunosorbent assay (ELISA), magnetic resonance imaging (MRI), radiolabeling, fluorescence spectroscopy, laser ablation inductively coupled plasma MS (LA-ICP–MS,) and size exclusion chromatography. These tools provide an invaluable way of examining a drug's journey through the body. By leveraging the most modern technologies, we are able to conduct a thorough survey of NDDSs and their various changes in structure, composition and form. This review can be beneficial for accurately assessing pharmacokinetics as well as gauging efficacy and safety profiles of new drug delivery systems. We hope this comprehensive overview will serve as an effective basis for application methodology when analyzing NDDSs.