The dependence of photoinduced carrier generation and decay on donor–acceptor nanomorphology is reported as a function of composition for blends of the polymer poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (pBTTT-C14) with two electron-accepting fullerenes: phenyl-C71-butyric acid methyl ester (PC71BM) or the bisadduct of phenyl-C61-butyric acid methyl ester (bis-PC61BM). The formation of partially or fully intercalated bimolecular crystals at weight ratios up to 1:1 for pBTTT-C14:PC71BM blends leads to efficient exciton quenching due to a combination of static and dynamic mechanisms. At higher fullerene loadings, pure PC71BM domains are formed that result in an enhanced free carrier lifetime, as a consequence of spatial separation of the electron and hole into different phases, and the dominant contribution to the photoconductance comes from the high-frequency electron mobility in the fullerene clusters. In the pBTTT-C14:bis-PC61BM system, phase separation results in a non-intercalated structure, independent of composition, which is characterized by exciton quenching that is dominated by a dynamic process, an enhanced carrier lifetime and a hole-dominated photoconductance signal. The results indicate that intercalation of fullerene into crystalline polymer domains is not detrimental to the density of long-lived carriers, suggesting that efficient organic photovoltaic devices could be fabricated that incorporate intercalated structures, provided that an additional pure fullerene phase is present for charge extraction.