Controlling the nanoscale arrangement in polymer-fullerene organic solar cells is of paramount importance to boost the performance of such promising class of photovoltaic diodes. In this work, we use a pseudo-bilayer system made of poly(2,5-bis(3-hexadecylthiophen-2-yl)thieno[3,2-b]thiophene (PBTTT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), to acquire a more complete understanding of the diffusion and intercalation of the fullerene-derivative within the polymer layer. By exploiting morphological and structural characterisation techniques, we observe that if we increase the film solidification time the polymer develops a higher crystalline order, and, as a result, it does not allow fullerene molecules to intercalate between the polymer side-chains. Gaining insight into the detailed fullerene intercalation mechanism is important for the development of organic photovoltaic diodes (PVDs).