The drive for the development of systems that can simultaneously investigate chemical and morphological information comes from the requisite to fully understand the structure and chemical reactivity relationships of materials. This is particularly relevant in photocatalysis, a field ruled by surface interactions. An in-depth understanding of these complex interactions could lead to significant improvements in materials design, and consequently, in photocatalytic performances. Here, we present a first approach to a combined atomic force microscopy (AFM) and Raman spectroscopy characterization of anodic TiO2 nanotubes arrays decorated with Ag nanoparticle electrodeposition from either the same anodizing organic electrolyte or from an aqueous one. Photocatalytic substrates were used in up to 15 consecutive photocatalysis tests to prove their possible deterioration with reuse. Sample aging can, in principle, produce changes in both the morphology and the chemical compounds that characterize the photocatalyst surface. Adopting multiple characterization techniques, such as a combination of AFM and Raman spectroscopy in an original setup, can profitably enable the observation of surface contamination. A significant drop in photocatalytic activity was observed after 10 cycles on samples where silver was deposited from the organic electrolyte, while the others remained stable. Such a drop was ascribed to photocatalyst deactivation. While in other cases, a simple recovery treatment allowed the initial photoactivity to be restored, this deactivation was not restored even after chemical and thermal cleaning treatments.