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The data provided in the article is in association with the journal article “Synthesis of cobalt oxide nanoparticles using endophytic fungus Aspergillus nidulans”. Characterization data (ultraviolet-visible (UV–vis) spectroscopy, dynamic light scattering (DLS) analysis, scanning electron microscopy (SEM), field emission gun scanning electron microscopy (FEGSEM)) of nanoparticles synthesized using different precursor concentrations (2 mM and 10 mM) have been presented in this article. Data obtained by t-test and F-test have been given for absorbance values exhibited by nanoparticles synthesized using different concentrations. Required figures and table have been depicted.