In this work, we investigate the effect of phase morphology on the nature of charges in poly(2,5-bis(3-tetradecyl-thiophen-2-yl)thieno[3,2,-b]thiophene) (pBTTT-C16) and phenyl-C61-butyric acid methyl ester (PC61BM) blends over timescales greater than hundreds of microseconds by quasi-steady-state photoinduced absorption spectroscopy. Specifically, we compare an essentially fully intermixed, one-phase system based on a 1 : 1 (by weight) pBTTT-C16 : PC61BM blend, known to form a co-crystal structure, with a two-phase morphology composed of relatively material-pure domains of the neat polymer and neat fullerene. The co-crystal occurs at a composition of up to 50 wt% PC61BM, because pBTTT-C16 is capable of hosting fullerene derivatives such as PC61BM in the cavities between its side chains. In contrast, the predominantly two-phase system can be obtained by manipulating a 1 : 1 polymer : fullerene blend with the assistance of a fatty acid methyl ester (dodecanoic acid methyl ester, Me12) as additive, which hinders co-crystal formation. We find that triplet excitons and polarons are generated in both phase morphologies. However, polarons are generated in the predominantly two-phase system at higher photon energy than for the structure based on the co-crystal phase. By means of a quasi-steady-state solution of a mesoscopic rate model, we demonstrate that the steady-state polaron generation efficiency and recombination rates are higher in the finely intermixed, one-phase system compared to the predominantly phase-pure, two-phase morphology. We suggest that the polarons generated in highly intermixed structures, such as the co-crystal investigated here, are localised polarons while those generated in the phase-separated polymer and fullerene systems are delocalised polarons. We expect this picture to apply generally to other organic-based heterojunctions of complex phase morphologies including donor:acceptor systems that form, for instance, molecularly mixed amorphous solid solutions, underlining the generality of the understanding gained here. © 2015 The Royal Society of Chemistry.