Gallium (Ga), in the form of gallium arsenide (GaAs) has been extensively used as a substrate in semiconductor materials. The use of microorganisms is fast becoming a promising alternative to not only leach the metal at low concentrations, but to do so in a more safe, environmental friendly as well as in an energy saving way. The metabolites such as peptides and proteins in Cellulosimicrobium funkei have previously been shown to be involved in GaAs leaching, however the mechanism of how they do this has not yet been fully elucidated. In this study, the role of C. funkei metabolites in the leaching of GaAs in different pHs was investigated. This study provides the first look at Ga-binding proteins from the supernatant of C. fimkei at different pHs using affinity chromatography and LC-MS/MS analysis. Additionally, the functional group of bacterial proteins involved in Ga-binding were investigated using Fourier transform infrared spectroscopy (FTIR) analysis. The FUR spectra revealed that Ga associated with the carboxylic groups of free amino acids/ peptides/ side chains of proteins, thiol-containing peptides/proteins, and the organic phosphate or aliphatic phosphate groups of phosphate binding proteins. This result was further confirmed by the identification of phosphate-binding proteins found in Ga-protein complexes by LC-MS/MS such as sugar ABC transporter proteins and protein kinases, with it possible that these proteins might improve Ga leaching efficiency. Furthermore, the type and number of proteins that could form Ga-protein complexes changed when the pH was changed, with the intensity of many proteins which could form Ga complexes increasing when the pH was increased. This was due to the amino acid side-chains in these proteins being deprotonated and therefore possessing a higher negative charge and allowing a better interaction possible with the positively charged Ga.