Neutrophilic, bacterial iron-oxidation remains one of the least understood energy-generating biological reactions to date. One of the reasons it remains under-studied is because there are inherent problems with working with iron-oxidizing bacteria (FeOB), including low biomass yields and interference from the iron oxides in the samples. In an effort to circumvent the problem of low biomass, a new large batch culturing technique was developed. Protein interactions with biogenic iron oxides were investigated confirming that such interactions are strong. Therefore, a protein extraction method is described to minimize binding of proteins to biogenic iron oxides. The combination of these two methods results in protein yields that are appropriate for activity assays in gels and for proteomic profiling.