The influence of short-term storage and spray- and freeze-drying of fresh microalgal paste on the stability of lipids and carotenoids of Phaeodactylum tricornutum was investigated. Furthermore, the effects of storage time (14 and 35 days) and condition (vacuum packed vs non vacuum packed, -20 °C vs 4 °C vs 20 °C) after spray- and freeze-drying were studied. Total lipid content, free fatty acid content, carotenoid content and degree of lipid oxidation were measured. No effects of spray- and freeze-drying and subsequent storage were found on total lipid content, except for short-term storage of the fresh microalgal paste, which led to pronounced lipolysis and therefore a lower total lipid content. Freeze-dried microalgae were found to be more susceptible to lipolysis upon storage than spray-dried microalgae. On the other hand, spray-dried microalgae were more susceptible to oxidation than freeze-dried microalgae, possibly due to breakdown of protecting carotenoids upon spray-drying. Hardly any effect of storage condition was observed for any of the parameters tested.