Electrified co-jetting of two aqueous polymer solutions followed by a thermal cross-linking step was used to create water-stable biphasic nanocolloids. For this purpose, aqueous solution mixtures of poly(acrylamide-co-acrylic acid) and poly(acrylic acid) were employed as jetting solutions. When the biphasic nanocolloids created by side-by-side electrified co-jetting were thermally treated, a cross-linking reaction occurred between amide groups and carboxylic groups to form stable imide groups. Infrared spectroscopy was employed to monitor the reaction. The quality and the integrity of the resulting biphasic nanocolloids were confirmed by confocal laser scanning microscopy, flow cytometry analysis, and dynamic light scattering. Selective encapsulation of two biomolecules in each phase of the biphasic colloids was maintained even after thermal reaction and suspension in aqueous environment. Well-dispersed spherical colloids with stable dye loadings in each hemisphere were kept intact without aggregation or dissolution for several weeks. Finally, biphasic nanocolloids were selectively surface-modified with a biotin-dextran resulting in water-stable particles to ensure binding of proteins only to a single hemisphere.