During the present time, anti-microbial features of copper (Cu) and zinc oxide (ZnO) nanoparticles (NPs) are extensively used to combat the growth of pathogenic microbes. CuNPs and ZnONPs are recurrently used in cosmetics, medicine and food additives, and their potential for toxic impacts on human and ecosystem is of high concern. In this study, the fate and toxicity of 16- to 96-nm-ranged biosynthesized copper (Bio-CuNPs) and zinc oxide (Bio-ZnONPs) was assessed in male Wistar rats. In vivo exposures of the two nanoparticles are achieved through two different administration routes namely, intraperitoneal (i/p) and intravenous (i/v) injections. The three different concentrations, no observable adverse effect concentration (NOAEC), inhibitory concentration (IC50) and total lethal concentration (TLC), were appraised at the dose range of 6.1 to 19.82 μg/kg and 11.14 to 30.3 μg/kg for Bio-CuNPs and Bio-ZnONPs respectively, for both i/p and i/v routes on 14th and 28th day of observation. These dose ranges are considered based on the previous study of antibacterial dose on multidrug-resistant pathogenic bacteria. In this study, we investigated the toxic effect of Bio-CuNPs and Bio-ZnONPs on animal behaviour, animal mass, haematologic indices, organ indices and histopathology of liver, spleen, kidney and brain organs. We found that i/v and i/p administration of Bio-ZnONPs in three different doses did not cause mortality and body weight was slightly reduced up to second week of administration compared with the vehicle control group. At the dose ranges of 11–16 μg/kg (i/v) and 24–30 μg/kg (i/p), no significant changes were observed in the serum creatinine level as well as serum ALT, serum AST level and ALP level which were 40.7 mg/dl, 37.9 IU/L and 82.4 IU/L normal as compared to vehicle control on 14th and 28th day of observation. These findings are confirmed in liver, kidney and spleen indices and histopathology studies. Furthermore, liver and kidney injury occurred when the concentrations of Bio-CuNPs were at 9.5 μg/kg (IC50) and 11.7 μg/kg (TLC) for i/v route of administration. Similarly, increase in serum ALT (67.7 mg/dl), AST level (70 IU/L) and ALP (128 IU/L) was also observed. And the body weight was significantly lower than in the control group after 14th day, and there were statistically significant differences observed by this route; interestingly, the toxicity of Bio-CuNPs in serum is prolonged (up to 28th day). Effect of Bio-CuNPs through i/p route was considerably low as compare to the control. Results of the present study revealed that Bio-ZnONPs have no effect on kidney and liver function biomarkers (both i/v and i/p) as compared to Bio-CuNPs.Graphical abstractAs shown in graphical abstract (Fig. 1), our aim is to assess the toxicity of Bio-CuNPs and Bio-ZnONPs through in vivo protocol. According to Kahru and Dubourguier reviews, AgNPs, CuNPs and ZnONPs have been historically used as biocides, for preventing the growth of microorganisms and algae (Kahru and Dubourguier 2010). Therefore, as like pesticides,...