Microalgae-derived esterified bio-oil can be an alternative energy source against the depletion of fossil fuel although the content of organonitrogen compounds (ONCs) can be high. Here, a metal–organic framework (MOF, MIL-101-NH2, with or without grafting ethylenediamine, ED) was modified to derive sulfonic acid-functionalized MIL-101 s. The obtained MOFs (including pristine MIL-101 and MIL-101-NH2), together with activated carbon (AC) as a reference, were utilized in adsorptive denitrogenation (ADN), especially the removal of carbazole (CBZ), one of the most difficult ONCs via hydrogenation or oxidation, from model fuel composed of methyl laurate. Although there was a study on ADN from model fuel composed of very light esters like methylacetate, there is no report using esters that are quite similar to fatty acid methyl esters of oils. Remarkably, MIL-101-NH-ED-SO3H, the first MOF having sulfonic acids on both the metal and linker sites, had noticeable maximum adsorption capacities (Qo) for the stubborn CBZ removal although the porosity is the lowest among the studied adsorbents. For example, Qo of the modified MOF was 205 mg/g which was higher than any studied adsorbents and was ca. 3 and 2 times that of AC and pristine MOF, respectively. The remarkable performance could be explained with H-bond (with a minor contribution of π-π interaction), based on calculations, FTIR, and functional groups of both the adsorbate and adsorbent. Furthermore, the recyclability of MIL-101-NH-ED-SO3H in CBZ adsorption was confirmed. Therefore, MOFs when adequately functionalized can be useful in ADN of fuel composed of esters.