Organic-inorganic nanocomposite films formed from blends of small-molecule organic semiconductors and colloidal quantum dots are attractive candidates for high efficiency, low-cost solar energy harvesting devices. Understanding and controlling the self-assembly of the resulting organic-inorganic nanocomposite films is crucial in optimising device performance, not only at a lab-scale but for large-scale, high-throughput printing and coating methods. Here, in situ grazing incidence X-ray scattering (GIXS) gives direct insights into how small-molecule organic semiconductors and colloidal quantum dots self-assemble during blade coating. Results show that for two blends separated only by a small difference in the structure of the small molecule forming the organic phase, crystallisation may proceed down two distinct routes. It either occurs spontaneously or is mediated by the formation of quantum dot aggregates. Irrespective of the initial crystallisation route, the small-molecule crystallisation acts to exclude the quantum dot inclusions from the growing crystalline matrix phase. These results provide important fundamental understanding of structure formation in nanocomposite films of organic small molecules and colloidal quantum dots prepared via solution processing routes. It highlights the fundamental difference to structural evolution which can be made by seemingly small changes in system composition. It provides routes for the structural design and optimisation of solution-processed nanocomposites that are compatible with the large-scale deposition manufacturing techniques that are crucial in driving their wider adoption in energy harvesting applications.