In a large non-stick skillet over medium heat cook the bacon until browned and crisp. Remove from the skillet onto a plate lined with paper towels.
Remove all of the bacon grease except for 1 tablespoon from the skillet. Add in the diced onions and sauté for 3 minutes. Add in the baby spinach and grated garlic and sauté until the spinach is wilted, about 2-3 minutes. Remove from the heat and set aside.
In a large bowl whisk together the eggs, egg whites, Dijon, thyme, nutmeg, milk, Greek yogurt, salt and pepper until combined.
Spray a 3-quart ceramic baking dish with cooking spray. Spread one-third of the bread cubes into the dish. Add one-third of spinach mixture, bacon and cheese. Repeat layering twice with remaining bread, spinach, bacon and cheese.
Pour the egg mixture evenly over the strata and cover the baking dish with plastic wrap. Refrigerate at least 8 hours or overnight.
The next day, let it stand at room temperature for 30 minutes while preheating the oven to 350°F. Bake the strata, uncovered, on the middle rack of oven until puffed, golden brown, and cooked through, 50 to 65 minutes. If the strata starts to get too brown on top, cover it loosely with a piece of foil. Let stand 5 minutes before serving.