Phase imaging in atomic force microscopy (AFM) is a useful technique for determining dissipative tip-sample interactions related to changes in the material surface properties such as local stiffness or adhesion. In this work, we applied both phase imaging and phase spectroscopy measurements to conducting polymer (polypyrrole) doped with either hyaluronic acid or chondroitin sulfate. As observed in previous studies, phase-separated regions correlating with the characteristic nodular topography of polypyrrole and attributed to crystalline (doped) and amorphous (undoped) regions were observed. However, through additional phase spectroscopy measurements, we show that the phase-separated regions can arise due to variation in attractive and repulsive tip-sample interactions across the polymer surface. We show that these attractive and repulsive interactions are dependent on the redox state and degree of doping and suggest that they are related to phase separation of the polymer surface charge and/or energy. The latter may have implications for these materials when under investigation in a fluid, or biological, environment. For example, such surface variations will play a role in electrostatic forces, which in turn can influence protein and cellular interactions.