Critical elements, such as rare earths, gallium, and germanium, are becoming increasingly important to the global economy due to the advancement of alternative energy and electronic technologies. Australia produces an estimated 30 million tonnes per year of alumina refinery waste (red mud), which contains an array of critical elements. Biomining could be the key to harnessing this untapped critical element supply, as current chemical separation methods are costly and environmentally damaging. This approach relies upon using identified microorganisms with a prior demonstration of critical element utilisation and the presence of these species across various mine waste sites. Candidate microorganisms include Pseudomonas putida, Shewanella oneidensis, Geobacter metallireducens, and Aspergillus niger. This study aims at identifying the Ga, La, Dy, and Ge binding capacities of P. putida and the proteins related to critical metal metabolism using bioinformatics and “omics” research. Initial proteomics analyses have identified 153 statistically relevant proteins associated with Ga interactions, including transcriptional regulation proteins associated with arsenic metal tolerance (ArsR1 and ArsH) and proteins previously identified as having metal-binding capacity. These include pyrroloquinoline quinone (PQQ) dependent alcohol dehydrogenases, which have previously demonstrated lanthanide dependence and binding capability. These proteins will be produced and tested for their potential use as biomaterials to recover Ga, which will pave the way for developing a sustainable method to recover this highly demanded element. This research could be used as a platform to create novel sustainable biomining solutions for the valorisation of alumina refinery waste.