Abstract Flocculation is a promising low-cost alternative to centrifugation for harvesting microalgae for bulk lipid production. However, little is known about the effect of the harvesting method on the lipid content on the one hand and the lipid extraction efficiency on the other hand. In this study, both total lipid content (and fatty acid composition and free fatty acid amount) and lipid extraction efficiency of Phaeodactylum tricornutum biomass were compared after harvesting using either alum or alkaline flocculation, or centrifugation. Alum and alkaline flocculation did not severely impact total lipid content when expressing results on ash-free dry weight basis to account for the salts transferred to the biomass during flocculation. The fatty acid composition does not change substantially and alum nor alkaline flocculation had any effect on the extraction efficiency when using a commercial solvent system. This study demonstrates that alkaline flocculation can be an excellent primary harvesting method for Phaeodactylum tricornutum without impacting the lipid extraction efficiency.