Bulk heterojunction (BHJ) layers based on poly(3-hexylthiophene-2,5-diyl) (P3HT) and [6,6]-phenyl C61 butyric acid methyl ester (PCBM) were fabricated by two methods: codeposition of P3HT/PCBM from a common solvent (conventional BHJ) and by sequential, layer-by-layer deposition of P3HT/PCBM from separate solvents (layer-evolved BHJ). Thermally annealed layer-evolved BHJ solar cells show power conversion efficiencies and electron/hole mobilities comparable to conventional BHJ solar cells. The nanomorphology of both active layers is compared in situ by transmission electron microscopy (TEM) using a multilayer cross-sectional sample architecture. No significant difference is observed between the nanomorphology of the conventional BHJ and layer-evolved BHJ material implying that the bulk heterojunction forms spontaneously and that it is the lowest energy state of the two component system.