A significant problem with implantable sensors is electrode fouling, which has been proposed as the main reason for biosensor failures in vivo. Electrochemical fouling is typical for dopamine (DA) as its oxidation products are very reactive and the resulting polydopamine has a robust adhesion capability to virtually all types of surfaces. The degree of DA fouling of different carbon electrodes with different terminations was determined using cyclic voltammetry (CV) and scanning electrochemical microscopy (SECM) approach curves and imaging. The rate of electron transfer kinetics at the fouled electrode surface was determined from SECM approach curves, allowing a comparison of insulating film thickness for the different terminations. SECM imaging allowed the determination of different morphologies, such as continuous layers or islands, of insulating material. We show that heterogeneous modification of carbon electrodes with carboxyl-amine functionalities offers protection against formation of an insulating polydopamine layer, while retaining the ability to detect DA. The benefits of the heterogeneous termination are proposed to be due to the electrostatic repulsion between amino-functionalities and DA. Furthermore, we show that the conductivity of the surfaces as well as the response toward DA was recovered close to the original performance level after cleaning the surfaces for 10–20 cycles in H2SO4 on all materials but pyrolytic carbon (PyC). The recovery capacity of the PyC electrode was lower, possibly due to stronger adsorption of DA on the surface.