Herein, we present periodic DFT-based calculations on the thiophene adsorption and reaction pathways over niobium carbide and nitride cubic face-centered (001) surfaces by considering both direct (DDS) and hydrogenating (HYD) routes for further desulfurization reactions and evaluate the implications for the mechanism of hydrodesulfurization (HDS). The theoretical studies were based on ultrasoft pseudopotentials and a plane-wave basis set and were performed with the help of the Quantum-ESPRESSO package. To understand the roles of both surfaces in the adsorption and desulfurization processes, various starting configurations for the adsorbed thiophene were tested and the energetically most stable ones were used in bond breaking studies. It was observed that thiophene adsorbs preferentially in a η-5 configuration by interacting with the nitride surface through its π-structure, whereas, on the carbide surface, thiophene was found to prefer a tilted η-1 configuration. Based on nudged elastic band (NEB) studies, our results suggest that the ring hydrogenation does not necessarily lead to a preference for the HYD pathway of thiophene desulfurization. Furthermore, surface and electronic effects were also evaluated. We have found that under ideal conditions the niobium nitride surface should present better performance for the desulfurization of thiophene than the carbide surface.