Two types of Zr6‐based metal‐organic frameworks (MOF), {Zr6O4(OH)4(C6H3(COO)3)2(HCOO)6} (MOF‐808) and {Zr6O4(OH)4(C24H15(COO)3)2(HCOO)6} (UMCM‐309) are investigated as heterogeneous catalysts in oxidative desulfurization reactions. Postsynthetic approaches targeting the removal of the coordinating formate ligands are applied to further improve the MOFs’ catalytic activity, resulting in the formation of additional ZrIV open sites. Thus, three modified MOFs, namely MOF‐808‐M, UMCM‐309‐M1, and UMCM‐309‐M2, are synthesized with larger numbers of open sites, as shown by CD3CN chemisorption monitored by Fourier‐transform infrared spectroscopy (FTIR), leading to higher catalytic activity. Even at low catalyst loading, MOF‐808‐M exhibits high catalytic activity in the oxidation of sulfur compounds as well as high selectivity and reusability.