Healthy Breakfast Casserole

This post may contain affiliate links. As an Amazon Associate, I earn from qualifying purchases. Please read my disclosure.

This healthy breakfast casserole is one of my favorite ways to start the day. It’s loaded with colorful veggies, protein-packed eggs, and just the right amount of melty cheese. It’s comforting, flavorful, and perfect for prepping ahead of time. Whether I’m feeding my family on a busy weekday or making brunch for guests, this recipe is always a hit!

I first made this casserole as a clean-out-the-fridge kind of meal, and it quickly became part of our regular breakfast rotation. It uses simple, whole ingredients like spinach, peppers, mushrooms, and eggs, and it’s super flexible, great for using up whatever produce you have on hand.

Not only is it easy to make, but it also happens to be naturally gluten-free, and so good for you thanks to all the veggies it’s filled with! Plus, you can bake it in a casserole dish for weekend brunch or divide it into muffin tins for quick, grab-and-go breakfasts during the week. However you serve it, this is one healthy breakfast recipe I know you’ll come back to again and again.

Latest Recipe Video!

🥘 Ingredients

Here’s what I use to make my healthy breakfast casserole. Everything is easy to find, and you can customize it based on what’s in your fridge.

Eggs: I use large eggs as the base of this casserole. They hold everything together and add a good dose of protein to keep us full all morning.

Veggies: I use a combination of mushrooms (my preference is button or cremini mushrooms), frozen spinach (thawed and squeezed dry), green and red bell peppers, and red onion. You can use any color bell peppers, yellow or white onions, any type of mushroom and fresh spinach if needed!

Seasonings: Simple seasonings are all that’s needed! I used fresh minced garlic, salt and pepper to add flavor to the sauteed veggies. If you don’t have fresh garlic, garlic powder will also work.

Milk Or Cream: For this version, I used heavy cream, but you can also use whole milk or half-and-half instead of heavy cream. You can also use a plant-based milk, just make sure it’s unsweetened and plain. Keep in mind that if you use a plant-based milk this casserole won’t be as rich.

Cheese: I love the combo of shredded cheddar and crumbled feta. You can swap in mozzarella, goat cheese, or whatever you have on hand. If you’re using shredded cheese, I recommend grating your own cheese for the best flavor and creamiest melt. To make this dairy-free, use a vegan cheese (keep in mind, it won’t melt as well), or leave out the cheese altogether – the dish will still work without it!

Olive Oil: I use both liquid and spray oil to cook the vegetables and coat the baking dish so the casserole doesn’t stick. Coconut oil or avocado oil would also work.

🔪 How To Make

My healthy breakfast casserole comes together in just a few simple steps. I usually prep the veggies the night before so I can get it in the oven first thing in the morning.

Prep: I start by preheating the oven to 350°F and lightly greasing a 7×11-inch casserole dish with olive oil or cooking spray.

Saute Veggies: In a large skillet, I heat the olive oil over medium heat, then add the diced onion. I cook it for 2–3 minutes until it softens, then stir in the garlic, bell peppers, and mushrooms. I let everything cook down until the veggies are tender and most of the moisture has evaporated, then remove the pan from the heat.

Whisk Eggs: While the veggies cool slightly, I whisk the eggs with milk, salt, and pepper in a large mixing bowl until fully combined.

Start Assembling: I drain any excess moisture from the cooked veggies and then spread them evenly into the bottom of the greased baking dish.

Layer: Then I layer the thawed and squeezed spinach on top. I pour the egg mixture over the veggies, making sure it’s evenly distributed.

Bake: Then I top everything with the shredded cheddar and crumbled feta. I bake the casserole uncovered for 35-45 minutes, or until the center is set and the top is lightly golden brown. I usually check it at 35 minutes, then give it a few more if the middle is still soft.

Cool: Once it’s done, I let it cool for 10 minutes so it firms up before slicing.

Serve: I cut it into 12 pieces and serve it warm, or save some for later in the week!

📖 Variations

Yes, I do often change up the veggies in this casserole depending on what I have on hand, but there are a few other ways I like to change the flavors too! Here are some of my favorites:

• Make It Spicy: If I want to add a little heat, I’ll add 1/8-1/4 teaspoon of crushed red pepper or cayenne pepper to the egg mixture, and serve it with some hot sauce too.
• More Protein: For even more protein, I’ll add in crumbled vegan sausage or cottage cheese.
• Mini Muffin Version: For grab-and-go mornings, I pour the mixture into a greased muffin tin instead of a casserole dish. They bake in about 18–20 minutes at 350 degrees F and are easy to store or freeze for later.
• Mediterranean Style: I’ve made a version with chopped sun-dried tomatoes, olives, spinach, and a sprinkle of oregano. It pairs perfectly with a side of roasted potatoes or a green salad.
• Spicy Southwest: For a Tex-Mex vibe, I add diced green chiles or jalapeños and top the casserole with pepper jack cheese. I’ll even add a handful of corn and black beans into the egg mixture itself!

🍽 Serving Suggestions

My healthy breakfast casserole is super filling on its own, but I love serving it as part of a larger spread when we have guests or weekend brunch. It pairs really well with my breakfast fruit salad or this kale smoothie for something light and refreshing on the side.

If I’m making it for lunch or dinner, I’ll add a simple salad like this cucumber tomato salad or serve it with roasted potatoes or air fryer Brussels sprouts. The casserole is also delicious with a slice of whole wheat toast or an avocado mash on the side.

🧊 Storage Directions

• Refrigeration: Once it’s cooled completely, I cut it into slices and store them in an airtight container in the fridge. It’ll keep for up to 4 days, and the flavor gets even better by the next morning.
• Freezing: If I’m freezing it, I wrap individual slices in parchment paper and then store them in a freezer-safe container or bag. It’ll keep for up to 3 months in the freezer. When I’m ready to eat, I thaw it overnight in the fridge and reheat as usual. It’s such a time-saver on busy mornings!
• Reheating: To reheat, I just pop a slice in the microwave for about 30–60 seconds, or warm it in a 350°F oven for 10–15 minutes if I’m reheating multiple servings. When heating from frozen, make sure to this dish to thaw overnight in the refrigerator, before warming in the oven.

❓Recipe FAQs

📋 Recipe Card