The current invention relates to a method of isolating polyunsaturated fatty acids containing lipids from a lipids containing biomass. The method involves providing a suspension of cells with a PUFAs-containing lipid; optionally lysing the cells; concentrating the suspension; adding base equivalents to the suspension based on the total dry matter present; feeding a continuous reactor with the suspension; and separating the lipids-containing light phase from the water and cell debris-containing heavy phase.