A study on the photocatalytic degradation of contaminants (salicylic acid and stearic acid) on titanium dioxide films overcoated with a few monolayers of silica is presented herein. A rather uncommon situation was observed, where the presence of the thin silica layers decreased the degradation rate of stearic acid while increasing that of salicylic acid. The results were explained by addressing the effect in the presence of silica films on the desorption of the intermediate products formed in the degradation of salicylic acid. This finding, which may apply also to other aromatic compounds, may have implications on the design and operation of photocatalytic devices for indoor applications, since ultrathin layers of silica are known to be formed over time on the photocatalyst. An interesting effect of the thickness of the silica sub-nanometre layer on the degradation rate of salicylic acid was explained in terms of gradual changes in the isoelectric point. If optimized, this effect can be utilized to precisely control adsorption or desorption and accordingly to induce specificity in the photocatalytic degradation of contaminants. A methodology for preparing a molecularly imprinting photocatalyst with an inert ultrathin layer in between the imprinted sites was presented. It was found that overcoating the area in between the imprinted sites preserved the benevolent effect of imprinting. While at present the imprinting effect was moderate, there is a reason to believe that this effect can be improved considerably by controlling the type of inert overlayer.