Hyperspectral imaging with enhanced darkfield microscopy (HSI-M) possesses unique advantages in its simplicity and non-invasiveness. In consideration of the urgent need for profound knowledge on the behavior and effects of engineered nanoparticles (NPs), here, we determined the capability of HSI-M for examining cellular uptake of different metal-based NPs, including nanosized metals (silver and gold, both citrate stabilized), metal oxides (copper oxide and titanium dioxide), and CdSe/ZnS core/shell quantum dots at subtoxic concentrations. Specifically, we demonstrated that HSI-M can be used to detect and semi-quantify these NPs in the ciliated protozoan Tetrahymena thermophila as a model aquatic organism. Detection and semi-quantification were achieved on the basis of spectral libraries for the NPs suspended in extracellular substances secreted by this single-celled organism, accounting for matrix effects. HSI-M was able to differentiate between NP types, provided that spectral profiles were significantly different from each other. This difference, in turn, depended upon NP type, size, agglomeration status, and position relative to the focal plane. As an exception among the NPs analyzed in this study, titanium dioxide NPs showed spectral similarities compared to cell material of unexposed control cells, leading to false positives. High biological variability resulted in highly variable uptake of NPs in cells of the same sample as well as between different exposures. We therefore encourage the development of techniques able to reduce the currently long analysis times that still hamper the acquisition of statistically strong data sets. Overall, this study demonstrates the potential and challenges of HSI-M in monitoring cellular uptake of synthetic NPs.