It depends on the microbes you are trying to preserve, some bacteria are much more fragile than others and most of those are probably killed by freezing and some of them don't keep as long with freeze-drying (lyophilization).
It's depends on how long you want to preserve the bacteria and also the type of it. If you want to save it for 2-8 weeks, you can store it in freezer with temperature 6 degrees but for longer preservation, lypholization is the best method