Microalgae utilized for experiments are often not produced by the researchers that are doing experiments with them. The microalgae are made storable through thermal or freeze-drying by the producer. In an industrial scaled process, because of efficiency reasons, microalgae would not be dried, but processed directly. With that, the question is, if drying already could change the composition or structure that much, that a process scaled up from laboratory to productive scale with fresh microalgae would be less efficient or even would not work at all. The effect of freeze drying on the extraction behavior for the species Scenedesmus rubescens was investigated. It was obtained in freeze-dried condition and again was delivered in fresh state. The utilized microalgae were extracted with n-hexane, without and with different pretreatments (acidic hydrolysis and hydrothermal carbonization) to examine the differences in the yields. In conclusion, it was demonstrated that freeze drying harms the cell wall and therefore this process already influences the quantity of extracted lipids. Depending on the harshness of the treatment process for cell wall disruption this might influence the extracted yield when the algae are not freeze-dried. The quality of the extracted lipids does not change when freeze-dried.