The clustering and diffusion of C71-butyric acid methyl ester (PC71BM) in poly(3-hexylthiophene) (P3HT) has been studied using single layer blend and bilayer organic field-effect transistors (OFETs) and by atomic force microscopy (AFM). P3HT:PC71BM blend based OFETs were found to undergo phase-segregation upon annealing, which was detectable as a fall in electron mobility with increasing annealing temperature. By employing carefully designed bilayer P3HT:PC71BM OFETs, the diffusion-properties of PC71BM in P3HT could additionally be inferred from electron mobility measurements. It was found that the prerequisite annealing temperatures for detectable PC71BM clustering and diffusion in P3HT was approximately 20 °C higher than for PC61BM. The diffusion coefficient of PC61BM in P3HT was found to be several times higher that that of PC71BM. The present work provides unique insights into the diffusion process of fullerenes in conjugated polymers and could prove highly valuable for future materials development and device optimization.