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Emulsion separation is of high relevance for filtration applications, liquid–liquid-partitioning of biomolecules like proteins and recovery of products from droplet microreactors. Selective interaction of various components of an emulsion with substrates is used to design microfluidic flow chambers for efficient separation of emulsions into their individual components. Our lab-on-a-chip device consists of an emulsion separation cell with an integrated silicon sensor chip, the latter allowing the detection of liquid motion via the field-effect signal. Thus, within our lab-on-a-chip device, emulsions can be separated while the separation process is monitored simultaneously. For emulsion separation a surface energy step gradient, namely a sharp interface between the hydrophobic and hydrophilic parts of the separation chamber, is used. The key component of the lab-on-a-chip system is a multilayer and multifunctional nanofilm structure which not only provides the surface energy step gradient for emulsion separation but also constitutes the functional parts of the field-effect transistors. The proof-of-principle was performed using a model emulsion consisting of immiscible aqueous and organic solvent components. Droplet coalescence was identified as a key aspect influencing the separation process, with quite different effects during separation on open surfaces as compared to slit geometry. For a detailed description of this observation, an analytical model was derived and lattice Boltzmann computer simulations were performed. By use of grazing incidence small angle x-ray scattering (GISAXS) interfacial nanostructures during gold nanoparticle deposition in a flow field were probed to demonstrate the potential of GISAXS for in situ investigations during flow.