Polaron formation plays a major role in determining the structural, electrical and chemical properties of ionic crystals. Using a combination of first principles calculations and scanning tunneling microscpoy/atomic force microscopy (STM/AFM), we analyze the interaction of polarons with CO molecules adsorbed on the rutile TiO2(110) surface. Adsorbed CO shows attractive coupling with polarons in the surface layer, and repulsive interaction with polarons in the subsurface layer. As a result, CO adsorption depends on the reduction state of the sample. For slightly reduced surfaces, many adsorption configurations with comparable adsorption energies exist and polarons reside in the subsurface layer. At strongly reduced surfaces, two adsorption configurations dominante: either inside an oxygen vacancy, or at surface Ti5c sites, coupled with a surface polaron.