Organisms that occupy environments contaminated by radionuclides such as Chornobyl, Ukraine, face putative detrimental effects. How radioactive pollution affects organisms, especially in early life, is not well studied in the wild. Our study focuses on two interconnected factors that might be altered due to radionuclide contamination of the environment and influence fitness: early-life diet and gut microbiota, an important physiological constituent tied closely to diet and host physiology. We quantified fitness components, diet, and gut microbiota from nestlings of two passerine birds, Great tit (Parus major) and Pied flycatcher (Ficedula hypoleuca), by sampling animals in nest-boxes located in contaminated and uncontaminated areas within the Chornobyl Exclusion Zone, Ukraine. We used amplicon sequencing to identify dietary insects and to quantify the bacterial diversity and composition of the birds’ gut microbiota. Environmental radiation had no effect on fitness components (body condition and brood size) of either species. Both species had greater diversity in dietary insects in contaminated areas. In both bird species environmental radiation was not associated with bacterial diversity of gut microbiome, however radiation was associated with composition of microbiome. Other ecological factors: forest type, brood size and age were associated with P. major gut microbiome composition but not in F. hypoleuca. Our data show comparable responses in diet and gut microbiome of two wild species when exposed to environmental radionuclide contamination. These results give valuable insight to ecological processes in contaminated environment.