Aqueous-Two Phase Systems (ATPS) is an important tool for the separation of biological entities as proteins, membranes, enzymes, among others. On the other hand, microfluidics is an emerging technology that studies and manipulates liquids either one single phase or dispersed fluids such as droplets at the micro or smaller scales. Applications of microfluidics in different areas such as molecular biology, biochemical analysis and bioprocess have increased in the last years. In this work, we proposed a droplet-based microfluidic approach to generate ATPS systems and to observe how two model proteins, native ribonuclease A (RNase A) and its PEGylated form (PEG-RNase A), behave and partition on these systems. Using polyethylenglycol (PEG) and potasium phosphate salts as the phase-forming chemicals, we were able to form ATPS systems inside the microfluidic device as commonly performed in conventional ATPS macrosystems. Even more, formation of ATPS systems in which one of the fluids was present as a droplet was also achieved. As expected, model proteins exhibited the same behavior as they do in a macrosystem, that is, they displaced to a particular phase according to their affinity for them. When native RNase A was placed in the salt-rich phase, it remained there, and migrated from the PEG-rich phase to the former. On its part, PEGylated RNase A remained in the PEGrich phase or migrated from salt-rich phase to the PEG-rich phase. These results open the possibility for a prospect of micro bioprocess to separate interest biomolecules.