In this research, the ureolytic fungi Neurospora crassa, Pestalotiopsis sp. and Myrothecium gramineum were investigated for the preparation of nanoscale copper carbonate and the role of fungal extracellular protein in such mineral formation. After incubation in urea-modified media, carbonate-laden fungal supernatants were used for the precipitation of copper carbonate, with experimental results agreeing closely with those obtained using geochemical modelling (Geochemist's Workbench). Compared with commercial and chemically synthesized copper carbonate, the minerals obtained using fungal supernatants were nanoscale and showed varying morphologies. It was found that extracellular protein played an important role in determining the size and morphology of the carbonate minerals precipitated, and after mixture with CuCl2 and resultant copper carbonate precipitation, more than 80% protein was removed from the N. crassa supernatant. Moreover, with addition of extracellular protein extracted from different fungal supernatants or standard bovine serum albumin, more than 96% of protein was removed by carbonate mineral precipitation. These results provide direct experimental evidence for the preparation of copper carbonate nanoparticles utilizing fungal ureolytic activity and show that fungal extracellular protein plays an important role in the formation and size of specific nano metal carbonates. Such a process provides opportunities for production of specific and/or novel metal carbonate nanoparticles of applied relevance, and as precursors of other useful biomineral products such as oxides.