Preheat oven to 350 °F (177 °C) and spray a 9-inch circular baking dish with cooking spray.
Cook bacon in a large skillet over medium-high heat until crispy. Remove bacon from the skillet and drain on a paper towel lined plate. Reserve the bacon drippings.
Add shallots to the drippings and sauté for 1 minute over medium-high heat. Add the mushrooms and thyme and cook until mushrooms have softened, about 5 minutes. Stir in spinach and cook until spinach has wilted, about 2 minute. Remove from heat, let stand for 10 minutes. Drain any excess liquid.
In a large bowl, whisk together milk, half and half, eggs, Parmesan cheese, salt, and pepper.
Using a wooden spoon, gently stir in the mushrooms and spinach mixture then pour entire egg mixture into prepared baking dish.
Break or cut bacon into crumbles and sprinkle on top of the egg mixture.
Bake for 45-55 minutes, or until filling is set. Let stand for 10 minutes before serving.
Notes
For paleo: use coconut milk or almond milk, omit half-and-half and up milk quantity to 1 1/3 cups.Slightly adapted from Cooking Light