If frozen correctly and consumed duly within a maximum of six months within freezing, pomegranate seeds should freeze fine. However, as with all frozen foods, it is always advised to carefully inspect them for signs of spoilage before consuming. With pomegranate seeds, it is actually quite easy to tell. If they give an odor that is off, and if they seem excessively mushy and are too slimy and slippery to handle, chances are that they have gone bad.