Despite being one of the most thoroughly characterised molecular crystals, hexamethylenetetramine (HMT) and its deuterated counterpart (DHMT), are still not fully understood, especially regarding anharmonic and nuclear quantum effects. In this work, an unprecedented combination of experimental techniques, including neutron and X-ray diffraction, inelastic neutron scattering, neutron transmission, and Compton scattering, all augmented ab initio by harmonic lattice dynamics calculations, was applied. The main question that motivated the presented work was the interplay between the phonon anharmonicity and isotope and nuclear quantum effects related to the zero-point energies of proton and deuteron. Signatures of the combined effects of isotopic substitution, temperature, anharmonicity and nuclear quantum effects were found in data from all experimental methods. In the case of neutron and X-ray diffraction, these signatures manifested as systematic discrepancies between the structural and atomic displacement parameters and thermal diffuse scattering obtained from harmonic lattice calculations and their experimental counterparts. To this end, an important effect was found that could not have been explained by the harmonic lattice modelling; the reverse Ubbelohde effect, i.e. the observation that deuteration decreases hydrogen bond length in HMT. In the case of neutron transmission, further discrepancies between theoretical predictions and experimental data were found at cryogenic temperatures. Finally, applying the diabatic theory of the local potential of the intermolecular hydrogen bond in HMT, it was possible to elucidate the degree of anharmonicity of the C–H···N bonds by relating it to the magnitude of the vibrational isotope effect for the C–H bond stretching observed in inelastic and neutron Compton scattering experiments. It was found that the combined nuclear quantum and anharmonic effects of the protons (deuterons) in hydrogen bonds in HMT (DHMT) manifest as systematic discrepancies between the ab initio predictions for the widths of nuclear momentum distributions and the experimental values.