It is shown that the effect of substrate heating on the photo conversion efficiency in vacuum-deposited small molecule organic solar cells is closely related to the improved free charge generation in ordered C-60 regions. The formation of these ordered regions strongly depends on the deposition sequence in the device and differs therefore between inverted and noninverted cells. Substrate-induced local fullerene ordering is found in small molecule: C-60 bulk heterojunctions (BHJs) deposited on pristine C-60 at elevated temperatures. This does not occur for BHJs deposited under identical conditions on pristine donor molecule layers, despite similar degrees of phase separation in both cases. These findings point to a hitherto unidentified advantage of inverted over noninverted solar cells that manifests itself in a higher charge separation efficiency.