Modeling in heterogeneous catalysis requires the extensive evaluation of the energy of molecules adsorbed on surfaces. This is done via density functional theory but for large organic molecules it requires enormous computational time, compromising the viability of the approach. Here we present GAME-Net, a graph neural network to quickly evaluate the adsorption energy. GAME-Net is trained on a well-balanced chemically diverse dataset with C1–4 molecules with functional groups including N, O, S and C6–10 aromatic rings. The model yields a mean absolute error of 0.18 eV on the test set and is 6 orders of magnitude faster than density functional theory. Applied to biomass and plastics (up to 30 heteroatoms), adsorption energies are predicted with a mean absolute error of 0.016 eV per atom. The framework represents a tool for the fast screening of catalytic materials, particularly for systems that cannot be simulated by traditional methods.