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Contamination of plastic particles in environmental and biological systems raises concerns regarding their potential negative impacts. Human exposure to microplastics (MPs) and nanoplastics (NPs) is increasing; however, some potential adverse health effects might remain unclear, due to analytical challenges in detecting trace concentrations. To address this, we propose a workflow for NPs assessment in biological samples combining three complimentary methods, namely inductively coupled plasma mass spectrometry (ICP-MS), X-ray fluorescence imaging (XFI), and imaging mass cytometry (IMC) to detect palladium-doped NPs (Pd-NPs). This approach was used to quantify the temporal distribution and accumulation of Pd-NPs in mouse models under different experimental conditions, dosages, and time frames. Acute exposure showed a clear particle excretion from the gastrointestinal tract into feces, while subchronic exposure led to tissue accumulation. This workflow enhances our ability to analyze and study NP uptake and biodistribution mechanisms down to the nanoscale in complex biological samples.