Covalent organic frameworks (COFs) are among the fastest-growing classes of materials with an almost unlimited number of achievable structures, topologies, and functionalities. The exact structure of layered COFs is, however, hard to determine due to an often significant mismatch between experimental powder X-ray diffraction (PXRD) pattern and predicted geometries. We attribute these discrepancies to an inherent disorder in the stacking of layered COFs, invalidating standard theoretical three-dimensional (3D) models. We have represented the structures of COF-1, COF-5, and ZnPc-pz by stacking layers following the Maxwell-Boltzmann energy distribution of their stacking modes. The simulated PXRD patterns of the statistical COF models are close to the experimental ones, featuring an unprecedented agreement in peak intensity, width, and asymmetry. The rarely considered ABC stacking mode proved to be important in layered COFs, as well as including solvent molecules. Our model also shows several general features in PXRD originating from the stacking disorder.