Oxidative desulfurization (ODS) removes organic sulfur compounds from liquid transportation fuels (including diesel and jet fuels) in a two-step process: (1) chemical oxidation to form sulfones and (2) adsorption (or extraction) of the sulfones onto a polar adsorbent such as alumina. Continued development of ODS is limited in part by a lack of understanding of how different sulfur types in real fuels respond to its constituent oxidation and extraction steps. We treated two JP-8 jet fuels (described by here as 3773 and 4177, respectively) using the two-step ODS process. These two fuels had similar physical properties and hydrocarbon compositions but differing sulfur contents: the 3773 fuel was 720 ppm(w), while that of the 4177 fuel sulfur content was 1400 ppm(w). For the two-step ODS process, we used activated carbon-promoted performic acid as the oxidant and activated alumina as the adsorbent. The complete ODS treatment reduced the sulfur content of the 3773 fuel to a level below the detection limits of our total sulfur analyzer (40 ppm(w)), implying >94% sulfur removal. However, ODS treatment reduced the sulfur content of the 4177 fuel to 350 ppm(w), or 75% sulfur removal. To investigate this discrepancy at the molecular level, we targeted sulfur compounds in the stock and treated fuels using one-dimensional gas chromatography and comprehensive two-dimensional gas chromatography with both sulfur selective detection and time-of-flight mass spectrometry. Initially, the 4177 fuel was dominated by a suite of compounds identified as sulfides, disulfides, and thiophenes (SDT), whereas the 3773 fuel was dominated by its benzothiophene (BT) content. The SDT compounds were easily oxidized, but the corresponding sulfones were not efficiently removed using the alumina adsorbent. The BT compounds were more resistant to oxidation than the SDT compounds, but the oxidized BT compounds were more efficiently removed using the adsorbent than either the BT compounds or oxidized SDT compounds. Development of ODS technologies should account for the different responses of different sulfur compounds to the oxidation and adsorption treatments.