Tailoring of the titania morphology is achieved by the combination of a triblock copolymer, acting as structure-directing agent, and a sol-gel chemistry enabling the incorporation of the provided inorganic material (titania) into the selected phase of the triblock copolymer. Spin-coating of the solution on FTO-coated glass, followed by plasma etching and calcination of the thin film results in the formation of self-encapsulated crystalline titania nanostructures. The fabricated nanostructures are coated stepwise with dye, conductive polymers and gold forming a functional multilayer stack. An advanced small-angle scattering technique probing the sample with X-ray synchrotron radiation under grazing incidence (GISAXS) is employed for the characterization of the preparation route, as scattering allows accessing the structure inside the multilayers. The tailored titania morphology is preserved during the preparation route towards the functional multilayer stack of a photovoltaic demonstration cell. Two clearly distinguishable structures originate from the substrate and the titania templated by the triblock copolymer; hence the other layers induce no additional structures. Therefore, this investigation provides the evidence that the effort spent to tailor the morphology is justified by the preservation of the self-encapsulated titania morphology that is created by the structure-directing agent throughout the functional multilayer stack build-up.