Microbial analysis of a 2X1000-tonne bio-heap leaching plant of Malanjkhand copper ore was done. Continuous monitoring of the micro-organism profile was done through conventional methods. The evolution of microbial population was done at quarterly intervals. The bacterial cultures were allowed to grow on Feo medium and FeSo medium. Three iron-oxidising acidophiles, namely, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans and three sulphur-oxidising acidophilic bacteria, namely, Acidithiobacillus caldus, Acidiphilum sps and Sulfobacillus sps were present in the heap leach liquor. AFM studies were conducted for estimation of bacterial cell dimensions and evaluation of possible mechanism for bio-leaching of copper ore. Copyright © 2013 Inderscience Enterprises Ltd.