The selective concentration of the contents in a microdroplet using spontaneous emulsification was proposed and demonstrated in a microfluidic channel. Aqueous microdroplets having a 40-μm diameter, in octane containing 100 mM of Span 80, shrank to 10 μm within 10 min with nanodroplet formation at the interface of the microdroplets. The microdroplets' contents either stayed in the microdroplet or partitioned into the nanodroplets, depending on their properties. The size and the hydrophobicity of the contents are two parameters that determine concentration/separation. In addition, this method was applied to a bound complex and free ligand (B/F) separation to demonstrate its applicability to biochemical analyses. Here we report the separation of water-soluble molecules in microdroplets for the first time. This method is expected to enhance the flexibility of the design of droplet analytical processes and widen their applicability.