Control over thin film growth (e.g., crystallographic orientation and morphology) is of high technological interest as it affects several physicochemical material properties, such as chemical affinity, mechanical stability, and surface morphology. The effect of process parameters on the molecular organization of perfluorinated polymers deposited via initiated chemical vapor deposition (iCVD) has been previously reported. We showed that the tendency of poly(1H,1H,2H,2H-perfluorodecyl acrylate) (pPFDA) to organize in an ordered lamellar structure is a function of the filament and substrate temperatures adopted during the iCVD process. In this contribution, a more thorough investigation of the effect of such parameters is presented, using synchrotron radiation grazing incidence and specular X-ray diffraction (GIXD and XRD) and atomic force microscopy (AFM). The parameters influencing the amorphization, mosaicity, and preferential orientation are addressed. Different growth regimes were witnessed, characterized by a different surface structuring and by the presence of particular crystallographic textures. The combination of morphological and crystallographic analyses allowed the identification of pPFDA growth possibilities between island or columnar growth.