Although engineered nanomaterial (ENM) uptake, transport and response mechanisms in plants have received increased attention in recent years, many questions regarding ENM risks to the environment and to food safety remain unanswered. The impact of ENM interactions with co-existing organic/inorganic contaminants, including secondary ENMs, remains poorly understood. The physiological and molecular response of zucchini (Cucurbita pepo L.) under conditions of nanomaterial combined treatments (NMCT) with binary combinations of nanoparticles (NPs) of cerium oxide (CeO2), lanthanum oxide (La2O3), copper oxide (CuO), and zinc oxide (ZnO) (500 mg L−1) and cadmium sulfide quantum dots (CdS QDs) (100 mg L−1) were tested (for 21 days, in vermiculite) and compared with the respective individual (NMIT) and bulk material (BMT) treatments. The ICP-MS results within specific tissues upon exposure to NMCT or NMIT demonstrated that the metal content varied significantly upon co-exposure, including instances of antagonistic effects; La uptake was significantly decreased (50–80%, compared to NMIT or NMCT) upon CeO2 NP co-exposure whereas La2O3 NPs caused a complete deregulation (2–5-fold higher) of Cu uptake upon CuO NP co-exposure. Expression analysis of genes previously shown as responsive to ENM exposure confirmed the involvement of the chloroplast in plant response; ORF31, an electron carrier down-regulated in all treatments, showed potential as a biomarker of exposure/effects. Principal component analysis on plant physiological and molecular response provided insight into the nature of phytotoxicity under NMIT and NMCT. This systematic approach is useful for characterizing the risk associated with ENMs, providing mechanistic interpretations and holistic perspectives for complex systems of contamination.