A method of preparing encapsulated cells for freeze-drying, the method comprising at least two consecutive incubation steps, wherein the encapsulated cells are incubated in each incubation step in an incubation solution containing cryoprotectant over a suitable period of time, wherein the concentration of cryoprotectant in the incubation solution is increased with each subsequent incubation step, wherein the encapsulated cells are bacterial cells or yeast cells, and wherein the cryoprotectant is a composition comprising skim milk, glycerol and trehalose, wherein in the composition skim milk is present in a concentration of 3% (w/v) to 8% (w/v), glycerol is present in a concentration of 0.5% (w/v) to 2% (w/v) and trehalose is present in a concentration of 5% (w/v) to 13% (w/v).