•The partitioning behavior of proteins in aqueous two phase systems was examined.•A linear correlation between the proteins partition coefficients was observed.•A semi-empirical model was applied to predict proteins partition coefficients.•The electrostatic energy is influenced by the solvent electrostatic properties.•The model shows a good predicting ability on proteins partitioning. The present work aims to achieve an additional insight into the protein partitioning behavior in aqueous two phase systems (ATPSs), together with a study on the viability of a semi-empirical model based on continuum electrostatics to predict the protein partition characteristics. The partitioning behaviors of 14 globular proteins, with different properties, were explored in three polymer/polymer ATPSs. By the Collander equation, a linear correlation between protein partitioning coefficients in all systems was observed. Using the semi-empirical model it was possible to predict the partitioning behavior of proteins. The electrostatic energy depends on the protein size and ATPSs characteristics and varies in agreement with the difference in phase dielectric constants. Linear correlation of nonpolar energy, and the solvent accessible surface area was observed. Polymer structure and concentration have a significant influence on model viability. A good qualitative prediction of preferred phase for studied proteins was observed.