The influence of the metal ion in the mesoporous metal trimesate MIL-100(Al(3+), Cr(3+), Fe(3+), V(3+)) on the adsorptive removal of N/S-heterocyclic molecules from fuels has been investigated by combining isotherms for adsorption from a model fuel solution with microcalorimetric and IR spectroscopic characterizations. The results show a clear influence of the different metals (Al, Fe, Cr, V) on the affinity for the heterocyclic compounds, on the integral adsorption enthalpies, and on the uptake capacities. Among several factors, the availability of coordinatively unsaturated sites and the presence of basic sites next to the coordinative vacancies are important factors contributing to the observed affinity differences for N-heterocyclic compounds. These trends were deduced from IR spectroscopic observation of adsorbed indole molecules, which can be chemisorbed coordinatively or by formation of hydrogen bonded species. On the basis of our results we are able to propose an optimized adsorbent for the deep and selective removal of nitrogen contaminants out of fuel feeds, namely MIL-100(V).