This study provides new insights into sustainable fuel production by upgrading bio-derived oxygenates by catalytic hydrodeoxygenation (HDO). HDO of ethylene glycol (EG), cyclohexanol (Cyc), acetic acid (AcOH), and phenol (Phe) was investigated using a Ni-MoS2/MgAl2O4 catalyst. In addition, HDO of a mixture of Phe/EG and Cyc/EG was studied as a first step towards the complex mixture in biomass pyrolysis vapor and bio-oil. Activity tests were performed in a fixed bed reactor at 380–450 °C, 27 bar H2, 550 vol ppm H2S, and up to 220 h on stream. Acetic acid plugged the reactor inlet by carbon deposition within 2 h on stream, underlining the challenges of upgrading highly reactive oxygenates. For ethylene glycol and cyclohexanol, steady state conversion was obtained in the temperature range of 380–415 °C. The HDO macro-kinetics were assessed in terms of consecutive dehydration and hydrogenation reactions. The results indicate that HDO of ethylene glycol and cyclohexanol involve different active sites. There was no significant influence from phenol or cyclohexanol on the rate of ethylene glycol HDO. However, a pronounced inhibiting effect from ethylene glycol on the HDO of cyclohexanol was observed. Catalyst deactivation by carbon deposition could be mitigated by oxidation and re-sulfidation. The results presented here demonstrate the need to address differences in oxygenate reactivity when upgrading vapors or oils derived from pyrolysis of biomass.