Changes in structure of protein molecules and water-in-oil (w/o) microemulsion aggregates were investigated using the large protein immunoglobulin G (IgG, MW 155,000) and an equivolume oil/water mixture composed of brine, sulfosuccinic acid bis [2-ethylhexyll ester (sodium salt) (AOT), and isooctane. The protein solution in the microemulsion phase was metastable: over time this solution changed, as protein and w/o droplets aggregated and precipitated to the interface between aqueous and organic phases. Such factors as AOT concentration, temperature, and salt concentration were found to influence the protein and surfactant structures in the microemulsion. Protein conformation was probed using circular dichroism spectroscopy whereas the microemulsion structure was determined from dynamic light scattering measurements. Protein conformation and microemulsion structure were found to have significant effects on protein stability in the microemulsion. The stabilizing effects of clusters formed at higher salt and/or ACT concentrations are discussed. IgG adopts an intermediate denatured state in the microemulsion phase close to the alternatively folded state known as the A state, with well-defined contacts in the tertiary structure immediately after phase equilibration. The change in protein conformation with time accompanied by the cluster growth eventually leads to the protein and surfactant transfer into a third, solid middle phase from the organic solution.