It is known that the complex coacervation (CC) of biopolymers can induce conformational and structural changes of the interacting macromolecules. However, effect of such changes on the localization of biopolymers within the complex coacervate phase is unknown. In this paper confocal laser scanning, bright-field microscopy, phase analysis, dynamic light scattering, turbidimetry, circular dichroism and fluorescence measurements were used to study CC in aqueous gum arabic (GA)/lysozyme (lys)/system at various GA/lys weight ratio (q), pH 7.0 and ionic strength 0.01. CC had a binding stoichiometry of 88 lys molecules complexed per GA molecule, whereas the binding constant is 1.33⋅107 M−1. Complexation enhance with the decrease of pH from 10 to 4.6 and become weaker when the temperature increases, indicating contribution of hydrogen bonds in stabilization of complexes. We demonstrate for the first time the formation of multilamellar structure in the aqueous GA/lys coacervate phase that is similar to the structure of multilamellar liposomes. The amount of concentric vicious layers in the coacervate droplets are maximum at q values corresponding to maximum yield of complex phase.The content of GA in the layers increases with the increase of q, and in the direction from periphery to center of coacervate droplets. CC leads to a spectacular changes in the helix content of lys. We assume that hydrophilic lys molecules interacting with polydisperse GA undergo complex molecular changes leading to formation of the unique multilamellar structure.