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.
- Roast the sweet potato slices until they’re just tender.
- Cook the bacon until crisp and slowly caramelize the onions.
- Roast the Brussels sprouts until lightly browned.
- Layer the vegetables over the sweet potato base.
- Whisk together the eggs, coconut milk and seasonings.
- Pour the egg mixture over the vegetables and bake until the center is just set.
- 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}
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
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Preheat your oven to 425°F. Lightly grease a 9x13-inch ceramic baking dish.
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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
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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.
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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.
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Reduce heat to medium-low and add the onions to caramelize. Cook 18-20 minutes, stirring occasionally, until deeply golden and jammy.
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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.
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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.
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Spread the Brussels sprouts, bacon and onions evenly over the roasted sweet potato layer, then pour the egg mixture evenly over everything.
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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.
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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.
I want to make this recipe, but was wondering if U can leave our the bacon. I have all the other ingredients. Thanks.
I’m sure you can and even add other ingredients 🙂
Would this freeze well if I cut it into serving size portions after its baked? Rather than keeping it refrigerated (up to five days) and having to eat it multiple times.
I haven’t made this yet but planning on it today!
Hi! How long and at what temp would you use to reheat the whole dish? ?T
I would say cover it with aluminum foil and reheat at 400 degrees until heated through, not certain how long.
Could you just roast the bacon, brussell sprouts, onions and sweet potatotes together?
Can you assemble this the night before and then cook in the morning? Or do things get soggy?
I haven’t tried it but I think it would work out just fine, let me know if you try it out!
Hi there,
Can you tell us the nutritional information for this dish? Thank you!
First things first. The results are delicious. But . . . It takes far longer to prep and cook than advertised. Give yourself at least 30 minutes to prep. Furthermore, 25 minute cook time left me with a runny middle. Had to put it back in for about 20 minutes upon arriving at brunch. Start to finish including the bake off to finish was nearly 2 hours. Short on time? I microwaved my sweet potatoes and spread them like a pie crust. So if you don’t take that shortcut add the time to prep the sweet potatoes and cook them–probably another 25 minutes.
This Breakfast Casserole is fantastic! I’m doing 7 day meal prep along with Whole30. One challenge is finding recipes for days 5-7 that will keep in the freezer. This one will work great.
I had to scurry the portions into the meal prep containers and whisk them away because I could have easily stood in the kitchen with a fork and went to town! 🙂 I had previously tried a frittata recipe (from a different site) that I didn’t care for because it was so dense and flavorless. The addition of coconut milk to the eggs keeps them fluffy and the flavor compliments the sweet potato.
I’m doing the prep and Whole30 with a friend who doesn’t care for brussel sprouts, so I replaced them with 3 cups of zucchini. I lightly sautéed cubed zucchini after the onions and it turned out great. Next time I’ll do brussel sprouts because I love them.
This one is a keeper. Thanks so much!
So happy you like it! Great to sub in different veggies to make it personalized 🙂
This is literally the most delicious recipe I’ve ever made!!! This will a new obsession and will be a go-to from now on. Thank you for sharing this recipe with the world!
I made this casserole for a Sunday class brunch. It smelled delicious and was totally gone by the time I got to the table!! I sauteed spinach (4 cups baby) instead of brussel sprouts and added chopped red bell pepper. It looked fabulous, festive and had many requests for the recipe. Thanks for making my paleo quest yummy and healthy.
That sounds so good! Love that you customized it to make it your own – this is one of those recipes you can make with so many different ingredients and it always seems to work out 🙂
Oh my gosh…. this is so delicious! Such a great combination of fall flavors. I love Brussels sprouts and sweet potatoes. Never would have thought to add them to a breakfast casserole! I just started meal prepping. This recipe is great for that – fairly simple to put together, makes a weeks worth of breakfasts, and it warms up well. Thank you for sharing it!
Have you ever made this without onions? I can’t eat onions, so wondering if it still has depth of flavor?