The three-dimensional (3D) optical imaging of nanoparticle distribution within cells and tissues can provide insights into barriers to nanoparticle transport in vivo. However, this approach requires the preparation of optically transparent samples using harsh chemical and physical methods, which can lead to a significant loss of nanoparticles and decreased sensitivity of subsequent analyses. Here, we investigate the influence of electrophoresis and clearing time on nanoparticle retention within intact tissues and the impact of these factors on the final 3D image quality. Our findings reveal that longer clearing times lead to a loss of nanoparticles but improved transparency of tissues. We discovered that passive clearing improved nanoparticle retention 2-fold compared to results from electrophoretic clearing. Using the passive clearing approach, we were able to observe a small population of nanoparticles undergoing hepatobiliary clearance, which could not be observed in liver tissues that were prepared by electrophoretic clearing. This strategy enables researchers to visualize the interface between nanomaterials and their surrounding biological environment with high sensitivity, which enables quantitative and unbiased analysis for guiding the next generation of nanomedicine designs.