Contrary to the commonly accepted notion that ammonia inhibits the hydrodesulfurization (HDS) of organosulfur compounds, an unexpected promotional effect of ammonia on the hydrodesulfurization of thiophene over amorphous-silica-alumina (ASA)-supported sulfides of CoMo (CoMo/ASA) and NiMo is reported. Addition of ammonia may increase the activity up to a factor of 1.5. The effect is specific to Co- and Ni-promoted MoS2 supported on an acidic amorphous silica-alumina support. Over CoMo sulfides supported on gamma-alumina and carbon, the HDS of thiophene is inhibited by ammonia. The effect is related to the presence of Bronsted acid hydroxyl groups on the amorphous silica-alumina support, as it is found that after ion-exchange with Na+ the HDS activity decreases with the NH3 partial pressure. A comparison of infrared spectra of adsorbed CO over alumina- and ASA-supported CoMo following various pretreatments (H2S/H-2 vs H2S/NH3/H-2) points to an electronic effect of the acidic ASA support on the active Co-Mo-S phase. It is speculated that the sulfur bond energy is increased due to this interaction. While the desulfurization of thiophene is sensitive to these changes, sulfur removal from (di)benzothiophene is not, and ammonia acts only as an inhibitor, likely due to the stronger adsorption of these reactants.