Complex coacervation of polyelectrolytes with surfactant micelles is a promising system for a wide range of applications. However, the development of “green coacervates” from bio-based surfactants and biopolymers has not yet been explored. Herein, complex coacervation of micelles from a bolaform sophorolipid biosurfactant with oppositely charged cationic polyelectrolytes (i.e., chitosan oligosaccharide lactate, poly (L-lysine) and poly(allylamine)) was investigated. Turbidity titration, light and scanning electron microscopy (SEM), dynamic light scattering (DLS), cryogenic transmission electron microscopy (cryo-TEM) and Small Angle X-ray Scattering (SAXS) were used to monitor the evolution of complex structures as a function of pH and polyelectrolyte concentration. Phase boundaries of the biosurfactant–polyelectrolyte systems were obtained and these revealed the feasibility of coacervation in water over a broad range of pH, from 5 to 9. The state of complexation was found to depend primarily on pH and concentration and the nature of the polyelectrolyte. Light microscopy and SEM demonstrated the associative macrophase separation, and cryo-TEM highlighted the influence of the desolvation level on the coacervate arrangement where two main structures were formed as a function of the coacervation stage, namely spherical particles and aggregates. The SAXS data demonstrated that the sophorolipid micelles maintained their structure integrity following their binding to the cationic polyelectrolyte.