Bio-oils are the liquid products from the pyrolysis of biomass, which captured pronounced attention and showed relevance as an alternative source of fuels and chemicals. Bio-oils are complex mixtures of a large number of components, mostly oxygenated compounds, including many different chemical functionalities, which require upgrading (removal of oxygen) to be useful as fuels. As acid or bifunctional metal/acid catalysts are used in upgrading, the components in the mixture will be subjected to many different chemical reactions, including, among others, decarboxylation, decarbonylation, dehydration, demethoxylation, hydrogenation, dehydrogenation, cracking, isomerization, and hydrogen transfer. Purely thermal reactions are also to be produced in upgrading processes. Thus, the set of chemical reactions is exceptionally intricate. This review provides broad information about the mechanisms of numerous reactions which can take place, based on a transversal view, that is, the emphasis is posed on the reactions and the corresponding descriptions embrace the different chemical groups.