Magnetite nanoparticles exhibit clear technological potential for biomedical applications. The objectives of this study were to synthesize magnetite-organic complex nanoparticles through the use of metal-reducing bacteria and characterize the mineralogical and surface chemical properties of these nanoparticles as well as to test their potential applications in biomedical technology with regards to their protein immobilization capacity. The microbially formed magnetite nanoparticles had a size of around 10 nm with a spherical shape and were coated with organics containing an abundance of reactive carboxyl groups without any chemical process for functionalizing them. These microbial processes may lead to a simple preparation of functional magnetite-organic complex nanoparticles which have benefits for biomedical applications.