Clean fuel legislation throughout the world is driving the demand for ultralow-sulfur (<10 ppm) diesel (ULSD) fuel. Even though hydrodesulfurization remains the preferred technology to produce ULSD, the high associated costs lead to an increased interest in alternative processes, such as oxidative desulfurization (ODS). Monitoring the reacting species throughout the process is helpful for developing and/or optimizing ODS processes, although this has been difficult in real samples (complex mixtures). In this study, a hydrotreated diesel was subjected to a three-step ODS process (involving oxidation, extraction, and polishing) and thoroughly characterized using two-dimensional gas chromatography (2DGC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The obtained detailed speciation before and after each process step allows for monitoring the conversion of all sulfur species and assessing the process selectivity. The detailed analyses revealed that sulfur species from all families are converted to the corresponding sulfones. Therefore, benzothiophene, dibenzothiophene, and benzonaphthothiophene sulfones represent 90% of the total sulfur after the oxidation step. The comprehensive characterization revealed that, unlike the conventional hydrodesulfurization (HDS) process, the studied ODS process is selective for the oxidation and removal of HDS refractory sulfur species, such as dibenzothiophene and its alkyl derivatives, and less selective toward conventionally reactive sulfur species, such as thiophenes or benzothiophenes. Therefore, ODS may be used as a complementary method to HDS to achieve ultralow sulfur levels. Hydrocarbon conversion was also investigated, and this molecular class seems largely unaffected by the studied process. Nitrogen compounds are removed after the first process step through oxidation and/or extraction.