Nitrogen-containing compounds (NCCs) such as indole (IND) and quinolone (QUI) in a model fuel were adsorbed over pristine and variously functionalized metal–organic frameworks (MOFs) (here, UiO-66 and −NH₂, −NH₃⁺, −COOH, −COONa, −OH, −SO₃H functionalized UiO-66s) to quantitatively understand the interactions between the adsorbates (IND and QUI) and UiO-66s. The adsorbed quantity of IND and QUI increased linearly with increasing number of H-acceptors and H-donors (for H-bond), respectively, on UiO-66s (excluding one MOF for each adsorption), confirming the importance of H-bonding in the adsorption. UiO-66-NH₃⁺ and UiO-66-NH₂ showed a deviated trend in the IND and QUI adsorption, respectively; this might be explained by cation−π interactions and base–base repulsion, respectively. Moreover, the QUI adsorption increased linearly with increasing number of acidic sites on the MOFs (excluding basic ones), also suggesting the importance of acid–base interactions. Finally, UiO-66-NH₃⁺ showed the highest adsorption for both IND and QUI among the studied MOFs, suggesting that introducing an ammonium group on MOFs can be one way to develop a competitive adsorbent for the adsorptive denitrogenation of fuels.