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The nano- and micron scale morphology of poly(3-hexylthiophene) (P3HT) and polystyrene-block-polyisoprene-block-polystyrene (PS–PI–PS) elastomeric blends is investigated through the use of ultra-small and small angle X-ray and neutron scattering (USAXS, SAXS, SANS). It is demonstrated that loading P3HT into elastomer matrices is possible with little distortion of the elastomeric structure up to a loading of ∼5 wt%. Increased loadings of conjugated polymer is found to significantly distort the matrix structure. Changes in processing conditions are also found to affect the blend morphology with especially strong dependence on processing temperature. Processing temperatures above the glass transition temperature (Tg) of polystyrene and the melting temperature (Tm) of the conjugated polymer additive (P3HT) creates significantly more organized mesophase domains. P3HT blends with PS–PI–PS can also be flow-aligned through processing, which results in an anisotropic structure that could be useful for the generation of anisotropic properties (e.g. conductivity). Moreover, the extent of flow alignment is significantly affected by the P3HT loading in the PS–PI–PS matrix. The work adds insight to the morphological understanding of a complex P3HT and PS–PI–PS polymer blend as conjugated polymer is added to the system. We also provide studies isolating the effect of processing changes aiding in the understanding of the structural changes in this elastomeric conjugated polymer blend.