Quantum dots (QDs) play an active role in triggering biological effects and should not be viewed as ordinary carriers for biomedical applications; therefore, the aim of this study was to investigate the molecular mechanisms involved in the saturating accumulation of non-targeted, carboxylated QDs, the related specific internalization pathways and the induced changes in the endocytotic cycle in NIH3T3 cells. We determined that the saturating accumulation of QDs suppressed the internalization of subsequently introduced QDs that had an identical chemical composition. However, the reinitiation of uptake was detected in the NIH3T3 cells after 8 h of incubation in medium without QDs. A very small suppressive effect of accumulated QDs was observed on uptake via the clathrin-mediated endocytosis pathway and macropinocytosis. In contrast, uptake via the caveolin-mediated pathway was almost completely prevented. Deeper insight into the suppression mechanism was obtained by transiently transfecting NIH3T3 cells with the plasmid pEGFP-C1-Caveolin-1. In these transfected cells, the usual intracellular presence of Caveolin-1 near the plasma membrane was not observed after long-term incubation with QDs. The putative application of QDs for diagnostic visualization in combination with certain anticancer substances was also evaluated. The QDs did not affect the intracellular photosensitization pattern of the amphiphilic molecule chlorin e6 in the case of photodynamic therapy. However, the saturating accumulation of QDs increased the resistance of NIH3T3 cells to the widely used anticancer drug cisplatin.