Nanoporous polymer particles (NPPs) prepared by mesoporous silica templating show promise as a new class of versatile drug/gene delivery vehicles owning to their high payload capacity, functionality, and responsiveness. Understanding the cellular dynamics of such particles, including uptake, intracellular trafficking, and distribution, is an important requirement for their development as therapeutic carriers. Herein, we examine the spatiotemporal map of the cellular processing of submicrometer-sized disulfide-bonded poly(methacrylic acid) (PMASH) NPPs in HeLa cells using both flow cytometry and fluorescence microscopy. The data show that the PMASH NPPs are transported from the early endosomes to the lysosomes within a few minutes. Upon cell division, the lysosome-enclosed PMASH NPPs are distributed asymmetrically between two daughter cells. Statistical analysis of cells during cytokinesis suggests that partitioning of particles is biased with an average segregation deviation of 60%. Further, two-dimensional difference gel electrophoresis (2D-DIGE) analysis reveals that 127 out of 3059 identified spots are differentially regulated upon exposure to the PMASH NPPs. Pathway analysis of the proteomics data suggests that ubiquitylation, a reversible modification of cellular proteins with ubiquitin, plays a central role in overall cellular responses to the particles. These results provide important insights into the cellular dynamics and heterogeneity of NPPs, as well as the mechanisms that regulate the motility of these particles within cells, all of which have important implications for drug susceptibility characteristics in cancer cells using particle-based carriers.