Abstract Spinel Li1[Li0.33Ti1.67]O4 is an attractive candidate for the use as anode material in Li-ion batteries. This work focusses on the structural changes of spinel Li1[Li0.33Ti1.67]O4 upon the exchange of Li-ions with protons leading to the composition H0.9Li0.1[Li0.33Ti1.67]O4. The structure has been determined by means of Fourier density difference analysis of neutron diffraction data on the protonated material, collected over a wide range of d-spacings with high counting statistics. The protons replace the Li-ions on the crystallographic 8a sites, and also occupy a fraction of the 48f sites that are located in the same ab-plane as the 8a sites. These positions suggest that the protons prefer to be located near the oxygen atoms. Based on these results, a strong influence on the properties as Li-ion battery electrode material may be anticipated. The small change in unit-cell dimension and the considerable amount of hydrogen that can be hosted in spinel Li1[Li0.33Ti1.67]O4 are favorable for the use as fuel-cell electrolyte material.