Preheat oven to 400°F. Spray (2) 12-cup muffin tins with non-stick cooking spray.
In a medium frying pan, cook the bacon pieces until crisp. Remove the cooked bacon to a paper towel lined plate using a slotted spoon. Reserve 1 Tablespoon of bacon fat in the pan. Add the shallots and cook over medium-low heat until softened, about 3-4minutes. Remove the pan from heat.
In a medium bowl, whisk together the eggs, heavy cream, fine sea salt, ground pepper, and ground nutmeg.
Unfold the puff pastry onto a lightly floured surface or parchment paper. Roll out to about 12 x 14 inches and cut each pastry into 12 even squares (do not worry about it being perfectly sized). Press each piece into the prepared cups of the muffin tins.
Spoon a small amount of softened shallots (about ½ teaspoon) into the bottom of each puff pastry lined cup. Over the shallots, divide the cooked bacon equally into all 24 cups. Add the finely shredded Havarti cheese equally and then fill each cup approximately ½ full with the egg mixture (about 1- 1 ½ Tablespoons in each cup).
Bake for 18-19 minutes or until the puff pastry is golden brown, the eggs are puffy, and a toothpick comes out clean when inserted into the center of the mini quiche.
Cool for a few minutes before removing from the pans and serving warm, garnished with thyme or sliced green onions.
