I know that some gardeners, with the best of intentions, destroy these vital shelters. It may be a good idea to take a look at all the places used by pollinators during the winter. This is one case in which a little untidiness may be a good thing.
Most bees are ground nesters; this means that they build their nests in the ground, preferably a bare spot, dry and sunny and not subject to flooding. Sometimes there is a patch large enough for a whole town of nests; other times, just a few square inches of soil free from vegetation fill the needs of one enterprising bee raising a family. The mother bee dies at the end of the season, her mission accomplished. Her babies will emerge from the nests next spring.
Bumble bees find some nook or cranny underground, perhaps under a tree root, a log, or even an old wall. The difference here is that the overwintering pollinator in this case is the adult, already mated and fertilized female which will start a whole new colony next spring.
One of my favorite bees, Augochlora pura, doesn’t nest underground. Instead it finds a dead log, whose bark is beginning to peel, and builds its nest under the bark. The younger generation emerges at the end of summer. They mate, and the new bees find shelter, once again, under loose tree bark. Many old dead logs serve as wintering shelter for this bee.
There is great beauty in the mechanism of how an ecosystem works. I relish this beauty so I find it easy to accept the visual impact of an “untidy” garden in need of some raking, re-sodding, log removal, leaf litter removal, etc.
Helping Native Pollinators Winter Over Sierra Club