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Step 1
Coat a 9x13-inch baking dish (or another 3-quart baking dish) with oil or cooking spray. Place the cubed bread in the baking dish in an even layer; set aside.
Step 2
Heat the oil in a large skillet over medium heat until shimmering. Add the leeks and 1/2 teaspoon of the salt. Cook, stirring occasionally, until tender, 5 to 7 minutes. Transfer to a small bowl.
Step 3
Add the bacon to the skillet and sauté until the fat is almost all rendered out and it begins to get crisp, about 10 minutes. Using a slotted spoon, transfer to a paper towel-lined plate to drain.
Step 4
Whisk the eggs, milk, mustard, thyme, remaining 1/2 teaspoon salt, and pepper together in a large bowl.
Step 5
Spread the bacon over the bread cubes, followed by the leeks. Sprinkle the fontina on top, then pour the egg mixture over the entire thing. Press down on the top gently, so that all of the bread cubes get soaked a bit with the egg mixture. Cover and refrigerate overnight or if baking immediately, let the casserole rest on the counter while you preheat the oven.
Step 6
Arrange a rack in the middle of the oven and heat to 350°F. If you made the casserole ahead, take it out of the refrigerator so it can warm on the counter while the oven heats.
Step 7
Bake uncovered until the edges are bubbling and the top begins to brown, 50 to 65 minutes. The baking time will be greatly dependent on the depth of dish you use. Check the interior with a knife; if it comes out clean, the custard is baked through. (Cover with aluminum foil near the end of baking if the top is already browned.) Let cool for 5 minutes before serving.