ALD, atomic layer deposition, is conventionally used to deposit smooth and conformal coatings from the gas phase onto surfaces. ALD onto organic substrates, however, may lead to precursor diffusion into the sample and sub surface deposition. Hence, ALD into polymer films could be used for the preparation of inorganic-in-organic nano-composite materials. However, harnessing this approach requires deep understanding of the mechanism that governs the precursor infiltration, nucleation and in-situ growth with respect to the process and matrix parameters. Here we investigate the effect of temperature and matrix crystallinity on the deposition. Generally, increasing the process temperature increases precursor reactivity and its diffusion into the film, but also decreases its retainment in the film. Accordingly, we find a parabolic dependence of mass accumulation on the temperature with an optimum, in the case of a P3HT matrix, at 68 °C. To study the effect of matrix crystallinity we spun films of polythiophene blends with controlled crystallinity. Using absorption measurements and HRSEM we find that the infiltration and deposition occurs through the amorphous regions. Interestingly, the more crystalline films present faster nucleation rates and less homogenous dispersion of the first ZnO grains. After several deposition cycles, however, the more amorphous films show higher mass accumulation. We speculate that crystalline regions could encourage initial nucleation by retaining the precursor inside the film. However, once nucleation centers are scattered in the film, the growth depends on the infiltration of the precursors and hence faster in the more amorphous films.