The envisaged upgrading of lignocellulosic biomass derived feedstocks (bio-oils) in dedicated units or by coprocessing in existing units of the refinery, to partially replace crude oil in the production of transportation fuels, is a topic that has been receiving much attention from both industry and academia in recent years. Regardless of lignocellulosic biomass origin, these feedstocks are complex mixtures of many oxygenated hydrocarbons. Therefore, their upgrading toward liquid fuels must include oxygen removal. So far, two main routes have been proposed, considering many studies at laboratory scale and others from industry: catalytic hydrotreatment (HDT), mainly hydrodeoxygenation (HDO), and catalytic cracking, technologies that are already present in today’s refineries configuration. HDO has been performed at high hydrogen pressure, using catalysts based on those typically applied in conventional hydrotreating, as well as a new type of supported noble metal and transition metal catalysts. Catalytic cracking occurs at atmospheric pressure, using acid catalysts, mainly the active phases of fluid catalytic cracking (FCC) catalysts (HY and HZSM-5 zeolites). The present review is then focused on the upgrading possibilities of renewable nonedible feedstocks, obtained from biomass fast pyrolysis or liquefaction, in petroleum refineries, toward the production of second generation biofuels. It includes the recent studies concerning the alternative of bio-oils coprocessing together with crude oil feedstocks. In fact, although all these feedstocks have the potential to be directly converted into transportation fuels in dedicated units, it seems more attractive to upgrade them in combination with conventional feedstocks.