The microstructure of blend films of conjugated polymer and fullerene, especially the degree of mixing and crystallization, impacts the performance of organic photovoltaic devices considerably. Mixing and crystallization affect device performance in different ways. These phenomena are not easy to screen using traditional methods such as imaging. In this paper, the amorphous regiorandom poly(3-hexylthiophene) is blended with the potentially crystalline fullerene [6,6]-phenyl-C61-butyric acid methyl ester PCBM and the amorphous bis-adduct. First, the degree of mixing of polymer: fullerene blends is evaluated using UV–Vis absorption, steady-state and ultra-fast photoluminescence spectroscopy. The blue-shift of the polymer emission and absorption onset are used in combination with the saturation of the polymer emission decay time upon fullerene addition in order to infer the onset of aggregation of the blends. Second, the crystallinity of the fullerene is probed using variable angle spectroscopic ellipsometry (VASE), electroluminescence and photoluminescence spectroscopy. It is shown that the red-shift of charge transfer emission in the case of PCBM based blends cannot be explained solely by a variation of optical dielectric constant as probed by VASE. A combination of optical spectroscopy techniques, therefore, allows to probe the degree of mixing and can also distinguish between aggregation and crystallization of fullerenes.