Much research has been carried out in the last decade to convert bio-based feedstock into fuels and chemicals. Most of the research focuses on developing active and selective catalysts, with much less attention devoted to their long-term stability. This Review considers the main challenges in long-term catalyst stability, discusses some fundamentals, and presents options for their mitigation. Three main challenges are discussed: catalyst fouling, catalyst poisoning, and catalyst destruction. Fouling is generally related to the deposition of insoluble components present in the feed or formed by degradation of the feed or intermediates. Poisoning is related to the deposition of electropositive contaminants (e.g. alkali and alkaline earth metals) on acid sites or of electronegative contaminants (e.g. N and S) at hydrogenation sites. Catalyst destruction results from the thermodynamic instability of most oxidic supports, solid acids/bases, and hydrogenation functions under hydrothermal conditions.