Paleo Breakfast Casserole {Whole30}

This Paleo Breakfast Casserole with bacon, sweet potatoes, Brussels sprouts and eggs is an easy Whole30 breakfast that’s perfect for meal prep, brunch and holiday mornings!

*This recipe was originally posted in 2016 and updated July 2026 with new photos plus improved instructions and tips for success.

Looking for a hearty breakfast that’s easy to make, packed with protein, and perfect for meal prep?

This Paleo Breakfast Casserole with Bacon & Sweet Potatoes is loaded with crispy bacon, roasted sweet potatoes, caramelized onions, Brussels sprouts, and fluffy baked eggs for a breakfast that’s both nourishing and incredibly satisfying!

Unlike traditional breakfast casseroles made with bread or cheese, this Paleo and Whole30-friendly version uses a layer of roasted sweet potatoes as the base, creating beautiful slices while adding natural sweetness and plenty of flavor.

It’s dairy-free, gluten-free, and ideal for everything from busy weekday breakfasts to holiday brunches.

Whether you’re feeding a crowd or stocking your refrigerator with grab-and-go breakfasts for the week, this casserole is a recipe you’ll find yourself making again and again.

Why You’ll Love This Paleo Breakfast Casserole

There are plenty of breakfast casseroles out there, but this one stands apart thanks to its combination of wholesome ingredients and incredible flavor.

You’ll love it because:

• High in protein to keep you full
• Paleo, Whole30, dairy-free and gluten-free
• Perfect for weekly meal prep
• Great for brunch, holidays or breakfast-for-dinner
• Loaded with vegetables
• Naturally flavorful without cheese
• Easy to make ahead

The roasted sweet potato base gives every slice structure while the crispy bacon, caramelized onions and Brussels sprouts create layers of savory flavor in every bite.

Ingredients You’ll Need

This breakfast casserole uses simple, wholesome ingredients that work together deliciously! Here’s everything you’ll need to prepare it:

Sweet Potatoes

Thinly sliced sweet potatoes roast into a tender, lightly caramelized base that supports the casserole and adds subtle sweetness.

Bacon

Sugar-free bacon brings smoky flavor and crispy texture while keeping the recipe Whole30 compliant.

Brussels Sprouts

Roasted Brussels sprouts add color, texture and extra vegetables without overpowering the casserole.

Yellow Onion

Slowly caramelized onions provide rich, naturally sweet flavor that pairs perfectly with the bacon.

Eggs

A dozen eggs create a fluffy, protein-packed casserole that’s satisfying enough for breakfast, brunch or even dinner.

Full-Fat Coconut Milk

Coconut milk keeps the eggs rich and tender while remaining completely dairy-free.

Nutritional Yeast

Adds a subtle cheesy flavor without any dairy.

Fresh Chives

A sprinkle of fresh chives after baking brightens both the flavor and presentation.

How to Make This Paleo Breakfast Casserole

Making this casserole is easier than you might think.

1. Roast the sweet potato slices until they’re just tender.
2. Cook the bacon until crisp and slowly caramelize the onions.
3. Roast the Brussels sprouts until lightly browned.
4. Layer the vegetables over the sweet potato base.
5. Whisk together the eggs, coconut milk and seasonings.
6. Pour the egg mixture over the vegetables and bake until the center is just set.
7. Finish with fresh chives before serving.

The result is a beautifully layered breakfast casserole that’s flavorful, filling and easy to slice!

What Can I Substitute for Brussels Sprouts?

When I was dreaming up this casserole, I knew I wanted to add some roasted GREEN veggies!  So, it was down to either Brussels sprouts or broccoli.  I decided on Brussels sprouts since I’m digging them lately, but in truth, you can sub your favorite veggie/veggies here and it will be delicious.

If you like, try including broccoli, mushrooms, peppers, asparagus – really anything roast-able! You can also add sautéed spinach or kale.

I also have a Mexican Breakfast Casserole that is Paleo and Whole30 if you want to spice things up a bit!

Why Should I Use Nutritional Yeast?

I wanted a little bit of a kicker in the form of CHEESY flavor.  Ever since trying out Amanda’s dairy free cheese sauce, I’ve been experimenting with adding nutritional yeast to a few of my favorites recipes. Nutritional yeast is a great way to get that cheesy flavor without adding unwanted dairy to your cooking.

While it has a subtle flavor, it definitely adds something to the egg mixture in this casserole and is a fun ingredients to experiment with if you typically avoid dairy or are doing the Whole30.

Tips for Success

Roast the sweet potatoes before assembling the casserole so they’re perfectly tender once baked.

Take the time to caramelize the onions slowly. They add incredible depth of flavor that makes this casserole taste special.

Don’t overbake the eggs. Remove the casserole as soon as the center is set to keep the texture soft and fluffy.

Allow the casserole to rest for about 10 minutes before slicing for clean, even servings.

Finish with fresh chopped chives after baking to add freshness and vibrant color.

Easy Variations

This recipe is flexible and easy to customize.

• Replace the bacon with breakfast sausage.
• Substitute broccoli or chopped kale for the Brussels sprouts.
• Add a pinch of crushed red pepper flakes for a little heat.
• If dairy isn’t a concern, sprinkle freshly grated Parmesan over the finished casserole.
• Add diced bell peppers for extra color and sweetness.

Make Ahead, Storage & Freezing

This Paleo breakfast casserole is perfect for meal prep.

You can prepare all of the components ahead of time, assemble the casserole, cover, and refrigerate overnight before baking.

Store leftovers in an airtight container in the refrigerator for up to 5 days. Individual slices reheat beautifully in the microwave, making them perfect for quick weekday breakfasts.

To freeze, allow the casserole to cool completely, then slice into individual portions. Freeze in airtight containers for up to 3 months and thaw overnight in the refrigerator before reheating.

Frequently Asked Questions

Can I make this Paleo breakfast casserole ahead of time?

Yes. Assemble the casserole the night before, cover tightly and refrigerate until you’re ready to bake.

Is this breakfast casserole Whole30?

Yes, as long as you use sugar-free, Whole30-compliant bacon, every ingredient is Whole30 approved.

Can I freeze this breakfast casserole?

Absolutely. Slice the cooled casserole into portions and freeze for up to 3 months.

Can I substitute another vegetable for Brussels sprouts?

Yes. Broccoli, kale, spinach or asparagus all work well in this recipe.

Can I use regular milk instead of coconut milk?

If you don’t need the recipe to be dairy-free or Paleo, whole milk or half-and-half can be substituted. For the best Paleo texture, use full-fat canned coconut milk.

Why do I roast the sweet potatoes first?

Roasting them first ensures they become tender and creates a sturdy base or “crust” that helps the casserole slice neatly after baking.

How long will leftovers keep?

Stored in the refrigerator, leftovers stay fresh for up to 5 days, making this an excellent meal prep breakfast.

Whether you’re planning a holiday brunch, prepping breakfast for the week, or simply looking for a wholesome way to start your morning, this Paleo Breakfast Casserole with Bacon & Sweet Potatoes is a recipe you’ll come back to again and again.

The combination of crispy bacon, roasted sweet potatoes, caramelized onions, Brussels sprouts, and fluffy baked eggs creates a satisfying breakfast that’s every bit as comforting as a classic casserole while staying completely Paleo, Whole30, dairy-free, and gluten-free.

If you make this recipe, I’d love to hear what you think! Leave a comment and star rating below, and if you share it on social media, be sure to tag me so I can see your delicious creation!

More Healthy Breakfast Recipes You’ll Love

If you’re looking for more make-ahead breakfast ideas, be sure to try:

• High Protein Chicken Sausage Breakfast Bowls
• Breakfast Meal Prep Bowls
• Whole30 Breakfast Hash
• Green Breakfast Bowls
• Favorite Paleo Breakfast Bowl
• Whole30 Italian Breakfast Casserole
• Ham and Veggie Breakfast Casserole

Paleo Breakfast Casserole with Bacon & Sweet Potatoes {Whole30}

This Paleo Breakfast Casserole with bacon, sweet potatoes, Brussels sprouts and eggs is an easy Whole30 breakfast that's perfect for meal prep, brunch and holiday mornings.

Author: Michele

Prep Time: 15 minutes

Cook Time: 1 hour

Total Time: 1 hour 15 minutes

Course: Breakfast/brunch

Cuisine: Whole30

Keyword: bacon, breakfast, brussels sprouts, caramelized onion, casserole, egg casserole, eggs

Servings: 10 servings

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4.63 from 310 votes

Ingredients

For the Sweet Potato Layer:

• 2 medium sweet potatoes about 1½ pounds, peeled
• 1 tablespoon avocado oil or olive oil
• 1/2 teaspoon fine sea salt
• 1/4 teaspoon black pepper
• 1/2 teaspoon garlic powder

For the Filling:

• 12 slices sugar-free bacon chopped
• 4 cups Brussels sprouts trimmed and thinly sliced
• 1 large yellow onion thinly sliced
• 1 tablespoon reserved bacon fat or avocado oil if needed

Egg Mixture:

• 12 large eggs
• 1/2 cup full-fat canned coconut milk
• 1/4 cup nutritional yeast
• 1 teaspoon garlic powder
• 1/2 teaspoon onion powder
• 1/2 teaspoon smoked paprika optional, but recommended
• 1 teaspoon fine sea salt
• 1/2 teaspoon black pepper

For Serving:

• 2 tablespoons chopped fresh chives
• Fresh cracked pepper

Instructions

1. Preheat your oven to 425°F. Lightly grease a 9x13-inch ceramic baking dish.
2. Using a mandoline or sharp knife, slice the sweet potatoes about 1/8-inch thick. In a large bowl, toss the slices with avocado oil, salt, pepper, garlic powder
3. Arrange the sweet potatoes in the baking dish in slightly overlapping rows until the bottom is completely covered. Roast for 20-25 minutes, until mostly tender and beginning to brown around the edges.
4. Meanwhile, cook the chopped bacon in a large skillet over medium heat until crisp. Transfer to a paper towel-lined plate. Reserve about 1-2 tablespoons bacon fat in the skillet.
5. Reduce heat to medium-low and add the onions to caramelize. Cook 18-20 minutes, stirring occasionally, until deeply golden and jammy.
6. While the onions cook, spread the sliced Brussels sprouts on a parchment-lined baking sheet and lightly toss with a drizzle of avocado oil and a pinch of salt and pepper. Roast for 12-14 minutes, just until tender with browned edges. They should still have some bright green color.
7. Lower the oven temperature to 375°F. In a large bowl, whisk together the eggs, coconut milk, nutritional yeast, garlic powder, onion powder, smoked paprika, salt, pepper until smooth.
8. Spread the Brussels sprouts, bacon and onions evenly over the roasted sweet potato layer, then pour the egg mixture evenly over everything.
9. Allow the casserole to sit for about 5 minutes so the eggs settle throughout, then bake in the preheated oven (375°F) for 28-33 minutes, until the center is just set and a knife inserted in the middle comes out clean, avoiding overbaking so the eggs stay soft.

10. Allow the casserole to rest for 10 minutes before slicing. Sprinkle generously with fresh chives and freshly cracked black pepper. Enjoy!

Recipe Video

Recipe Notes

Storage:
Refrigerate leftovers in an airtight container for up to 5 days.
Reheat individual portions in the microwave for 45-90 seconds.

Freezing:
Freeze individual portions in airtight containers for up to 3 months.
Thaw overnight in the refrigerator before reheating.

Nutrition

Calories: 287kcal

Carbohydrates: 16g

Protein: 13g

Fat: 20g

Saturated Fat: 8g

Polyunsaturated Fat: 3g

Monounsaturated Fat: 8g

Trans Fat: 0.1g

Cholesterol: 214mg

Sodium: 635mg

Potassium: 494mg

Fiber: 3g

Sugar: 4g

Vitamin A: 7023IU

Vitamin C: 32mg

Calcium: 67mg

Iron: 2mg

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