AbstractIn this study, transmission electron microscopy (TEM) and cryo‐scanning electron microscopy (cryo‐SEM) were evaluated for their ability to detect lipid bodies in microalgae. To do so, Phaeodactylum tricornutum and Nannochloropsis oculata cells were harvested in both the mid‐exponential and early stationary growth phase. Two different cryo‐SEM cutting methods were compared: cryo‐planing and freeze‐fracturing. The results showed that, despite the longer preparation time, TEM visualisation preceded by cryo‐immobilisation allows a clear detection of lipid bodies and is preferable to cryo‐SEM. Using freeze‐fracturing, lipid bodies were rarely detected. This was only feasible if crystalline layers in the internal structure, most likely related to sterol esters or di‐saturated triacylglycerols, were revealed. Furthermore, lipid bodies could not be detected using cryo‐planing. Cryo‐SEM is also not the preferred technique to recognise other organelles besides lipid bodies, yet it did reveal chloroplasts in both species and filament‐containing organelles in cryo‐planed Nannochloropsis oculata samples.