Embodiments of methods for purifying a biomass-derived pyrolysis oil are provided. The method comprises the step of contacting the biomass-derived pyrolysis oil with a first deoxygenating catalyst in the presence of hydrogen at first predetermined hydroprocessing conditions to form a first low-oxygen biomass-derived pyrolysis oil effluent. The low-oxygen biomass-derived pyrolysis oil effluent is contacted with an ionic liquid to remove phenolic compounds, nitrogen compounds and other impurities. This ionic liquid step may be followed by a second deoxygenation step or the deoxygenating may be completed and then followed by the ionic liquid purification step.