We studied the adsorption and diffusion of the prototypical n-type semiconducting fullerene molecule, C60, inside the pores of the p-type semiconductor, phthalocyanine phenylene-bis(boronic acid) (Pc-PBBA), a member of the class of two-dimensional covalent organic framework (COF) materials. This C60/Pc-PBBA system is an example of an ordered p–n heterojunction suitable for photovoltaic solar cell applications. We found that the small 1.7 Å lateral offset present between COF layers leads to discrete adsorption sites inside the pore, forming essentially a periodic ‘lattice’ on which the fullerene diffuses. By categorising the location of such lattice sites, we found the maximum theoretical packing density of fullerene in representative helical, zigzag and staircase Pc-PBBA stacks, as well as an average packing density in randomly stacked Pc-PBBA layers. All these simulated packing densities (51% of bulk) closely matched related experimental results by Dogru et al. [M. Dogru, M. Handloser, F. Auras, T. Kunz, D. Medina, A. Hartschuh, P. Knochel, T. Bein. A photoconductive thienothiophene-based covalent organic framework showing charge transfer towards included fullerene. Angew Chem Int Ed. 2013;52:2920–2924]. (49% of bulk) for a similar fullerene–COF system, [6,6]-phenyl-C61-butyric acid methyl ester/thienothiophene–COF, which produced a low power conversion efficiency. This shows that there is little improvement to be made to the electron transport in terms of fullerene packing density. We present values of the barriers for all diffusion pathways between neighbouring lattice sites categorised uniquely by a set of symmetry rules. Knowledge of these barriers allows us to generalise fullerene transport mechanisms within the Pc-PBBA pore. We observe that diffusion along the (vertical) pore axis is faster than (lateral) diffusion perpendicular to the pore axis; this will facilitate pore filling.