Herein, we examined the effect of finite size and wettability on the structural dynamics and the molecular arrangement of the propylene carbonate derivative, (S)-(-)-4-methoxymethyl-1,3-dioxolan-2-one (assigned as s-methoxy-PC), incorporated into alumina and silica porous templates of pore diameters d = 4 nm-10 nm using Raman and broadband dielectric spectroscopy, differential scanning calorimetry, and x-ray diffraction. It was demonstrated that only subtle changes in the molecular organization and short-range order of confined s-methoxy-PC molecules were detected. Yet, a significant deviation of the structural dynamics and depression of the glass transition temperatures, Tg, was found for all confined samples with respect to the bulk material. Interestingly, these changes correlate with neither the finite size effects nor the interfacial energy but seem to vary with wettability, generally. Nevertheless, for s-methoxy-PC infiltrated into native (more hydrophilic) and modified (more hydrophobic) silica templates of the same nanochannel size (d = 4 nm), a change in the dynamics and Tg was negligible despite a significant variation in wettability. These results indicated that although wettability might be a suitable variable to predict alteration of the structural dynamics and depression of the glass transition temperature, other factors, i.e., surface roughness and the density packing, might also have a strong contribution to the observed confinement effects.