The development of covalent organic frameworks (COFs) during the past decades has led to a variety of promising applications within gas storage, catalysis, drug delivery, and sensing. Even though most described synthesis methods result in powdery COFs with uncontrolled grain size, several approaches to grow COF films have recently been explored. However, in all COFs so far presented, the isolated materials are chemically homogeneous, with all functionalities homogeneously distributed throughout the entire material. Strategies to synthetically manipulate the spatial distribution of functionalities in a single film would be game changing. Specifically, this would allow for the introduction of local functionalities and even consecutive functions in single frameworks, thus broadening their synthetic versatility and application potential. Here, we synthesize two 3D crystalline COF films. The frameworks, the ionic B-based and neutral C-based COFs, have similar unit cell parameters, which enables their epitaxial stacking in a layered 3D COF film. The film growth was monitored in real time using a quartz crystal microbalance, showing linear growth with respect to reaction time. The high degree of polymerization was confirmed by chemical analysis and vibrational spectroscopy. Their polycrystalline and anisotropic natures were confirmed with grazing incidence X-ray diffraction. We further expand the scope of the concept by making layered films from COF-300 and its iodinated derivative. Finally, the work presented here will pave the path for multifunctional COF films where concurrent functionalities are embedded in the same crystalline material.