Despite several studies addressing nanoparticle (NP) interference with conventional toxicity assay systems, it appears that researchers still rely heavily on these assays, particularly for high-throughput screening (HTS) applications in order to generate “big” data for predictive toxicity approaches. Moreover, researchers often overlook investigating the different types of interference mechanisms as the type is evidently dependent on the type of assay system implemented. The approaches implemented in the literature appear to be not adequate as it often addresses only one type of interference mechanism with the exclusion of others. For example, interference of NPs that have entered cells would require intracellular assessment of their interference with fluorescent dyes, which has so far been neglected. The present study investigated the mechanisms of interference of gold NPs and silver NPs in assay systems implemented in HTS including optical interference as well as adsorption or catalysis. The conventional assays selected cover all optical read-out systems, that is, absorbance (XTT toxicity assay), fluorescence (CytoTox-ONE Homogeneous membrane integrity assay), and luminescence (CellTiter Glo luminescent assay). Furthermore, this study demonstrated NP quenching of fluorescent dyes also used in HTS (2′,7′-dichlorofluorescein, propidium iodide, and 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethyl-benzamidazolocarbocyanin iodide). To conclude, NP interference is, as such, not a novel concept, however, ignoring this aspect in HTS may jeopardize attempts in predictive toxicology. It should be mandatory to report the assessment of all mechanisms of interference within HTS, as well as to confirm results with label-free methodologies to ensure reliable big data generation for predictive toxicology.