The aim of study was to assess the joint effects of engineered nanoparticles (ENPs) in soil-plant system. The single and binary mixtures of nano-ZnO and nano-CuO at dose of 300 mg kg−1 were added to soil. The combined treatments of metal salts were applied to evaluate nano-specific effects. The bioavailable fraction of Zn/Cu was extracted with CaCl2 or DTPA from soil after 1, 7, 30 days. The plant response regarding to metal content, enzyme activity (SOD, POD, CAT) and relative gene expression (Zn/Cu SOD, CAT, APX, GPX) to ENPs mixtures was determined. The extractable metal concentrations in soil under co-exposure of ENPs were lower than under single treatments. The opposite combined effect was noticed for metal salts. After 7 days, lower Zn content in leaves was measured after co-exposure of ENPs than nano-ZnO, whereas in older plants the tendency was opposite. The highest Cu content in leaves was noted under co-exposure of metal salts, other treatments provided the similar Cu content level. The activity of enzymes was dependent on their type, sources of metal, duration and type of exposure. APX gene expression was only affected by ENPs. The study shed light on the interactions of ENPs in soil and plant.