Polymer-modified mortars are cementitious materials that integrate polymers from 5 to 20 wt.%. Those materials are widely used for protecting and/or repairing concrete surfaces among which building facades, civil engineering structures, or sewage networks. In this context, polymer-modified mortars are applied into thin layers of about 1–3 cm. However, previous studies performed regarding such materials were carried out on massive pieces and did not consider the interactions between polymer-modified mortars and microorganisms. Nevertheless, such interactions can lead to undesired aesthetical or structural modifications of those materials. As a result, the main objective of this paper is to evaluate the resistance to biocolonisation of polymer-modified mortars applied into thin layers in environmental conditions that are representative of the on-site applications. Two formulations of polymer-modified mortars and a polymer-free mortar are characterised in the hardened state. Then, the resistance of those mortars to biocolonisation is tested by means of two laboratory accelerated tests. The first experiment is performed in order to recreate biofouling at the surface of the specimens, while the second one exposes the materials to biodeterioration. The results and analyses show that in the presence of polymer, both porosity and capillary absorption of mortars are reduced, but this does not allow preventing or slowing down biocolonisation. In addition, this study suggests that the nature of the polymer has an influence on bioreceptivity of polymer-modified mortars. Finally, our results suggest that in the presence of polymer, the global material may have an improved inner cohesion.