The objectives of this study were, firstly, to adsorb biopolymer complexes to an emulsion interface through electrostatic interactions and, secondly, to test the stability of the emulsions covered with biopolymer complexes. Whey protein isolate (WPI)–apple pectin complexes made by thermal treatment (85 °C, 20 min) were successfully adsorbed to the interface of an oil-in-water emulsion stabilized with whey proteins. The stability of the emulsion covered with the WPI-pectin complexes was tested by measuring salt (0–500 mM NaCl), heat (40–90 °C, 30 min) and freeze-thaw (−20 °C, 22 h) stability at pH 3.5–4.5. The results revealed that the adsorption of WPI-pectin complexes to the emulsion interface led to the formation of stable emulsions. The most remarkable result was at pH 4.5, where the base emulsion (without biopolymer complexes) was aggregated, but became stable after the deposition of the WPI-pectin complexes. Emulsions covered with WPI-pectin complexes were stable to salt additions up to 200 mM, but aggregated at the 500 mM level of NaCl. They were also resistant to heat treatments, and no aggregation was observed. However, the adsorption of WPI-pectin complexes to the emulsions did not improve the freeze-thaw stability, on the contrary, they showed major aggregation. These results demonstrated that biopolymer complexes can be used to assemble hierarchial emulsion structures and, improve the emulsion stability to environmental stresses.