Klebsiella aerogenes can utilise monazite or xenotime as the only source of phosphate by dissolving the insoluble phosphate content using organic acids. As a result, a proportion of the rare earth element (REE) in these minerals is also released into the aqueous solution. Greater leaching of REE by K. aerogenes is achieved when the microbe is in direct contact with the mineral surface. This study demonstrated that K. aerogenes microcolonies and biofilm are selectively formed on and around the physical imperfections sites. However, no selective attachment was found for specific chemical or mineral composition. K. aerogenes produce extracellular DNA (eDNA). eDNA facilitates the initial attachment of bacteria to the surface of the mineral as a component of the extracellular polymeric substances. When pure eDNA was used to precondition the surface of the mineral, it inhibited bacterial attachment, most likely due to the repulsive electrical charge interaction between the bacteria and preconditioned surface, as both had a relatively similar net negative charge. The eDNA production varies for different mineral compositions. K. aerogenes produced a higher amount of eDNA on monazite compared to xenotime. K. aerogenes activities on the surface led to erosion of some of the mineral grains. Electron microscopy analysis revealed some disintegration of the mineral surface on the interface of bacteria and the mineral. There was also evidence of a carbon compound at the minerals' deep subsurface (10 micron deep). Both of these observations could be originated from microbial activity. Mass spectrometry of the microbial residues of the surface showed small signals for REE-organic acid complexes. Further understanding of the microbial biofilms on phosphate minerals during bioleaching and further analysis of the microbe-mineral interface, the surface and subsurface are essential to shedding light on the bioleaching mechanism.