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.
Wow this is so, so good! Customized the ingredients a little more to my liking. Used red potatoes, sliced and cooked in microwave. Roasted the brussels on the stove, added some kale and spinach. Added some cheese and no-salt seasoning to the eggs. Loved it!!
That’s great! Sounds delicious 🙂
Hi Michele!
This recipe sounds amazing and I will definitely try it, since I love all the ingredients included. Was wondering though, have you ever tried making this in a slow cooker? Thanks!
Nope I haven’t tried and I’m not sure about the time due to the eggs and not wanting to overcook, but I would think it’s possible as long as you get the timing right!
This looks so good but my husband despises sweet potatoes. Is there another option that tastes just as good? ?
You can probably use regular white potatoes with good results, haven’t tried it this way but it’s worth a shot. Also, you might want to look into Japanese sweet potatoes which are starchier and sort of a cross between sweet and white potatoes (and my absolute favorite!) They’re purple inside and white/yellowish inside.
This casserole is so, so yummy!!!!! I made it for the first time yesterday after seeing it on @wholefoodfor7 feed. I have it pegged for my breakfasts all week and I’m already looking forward to making another batch this weekend. Can’t wait to try many more recipes on your awesome website. Thank you!!
This recipe is 100 percent a breakfast win for me! I can eat eggs ’til the ends of the earth – fortunately for a Whole30 participant. However, when I’m not on W30, those eggs come with some pretty unhealthy drivethru runs because I don’t have time to make something every morning; I’m not a fan of hard boiled eggs that have sat in fridge for a week, and for some reason every frittata recipe I ever tried make the eggs taste weird. I’ve done breakfast muffins, too, and I don’t like the flavor of the eggs. I’ve been desperately searching for a healthy breakfast meal for years. I’ve finally found it here! Not only was this an easy time-saver cuz I could make a batch of twelve servings, freeze some, and have two weeks worth of breakfasts,
but I’m also a fan of how easy the recipe is to customize. To be clear, it is perfectly delicious as is. Now that I’m done with my January W30, though, I’ve made it with spinach, crumbled spicy breakfast sausage, and a very thin layer of Swiss cheese. It is SO good! Thank you for helping to provide me with the type of breakfast that suits my lifestyle – incredibly flavorful and fast. A true breakfast win!
I like your version! This is definitely one of those recipes that anyone can customize to their liking! Happy you really enjoyed it 🙂
Hi Michele,
I’m sorry I didnt know where to reply in a new box, but I was wondering if it’s possible to keep this in the refrigerator instead of the freezer, overnight before the final baking process. I would like to make this the night before a breakfast brunch at my office, but would rather not freeze it. Please let me know.
thank you so much!
Kim
I do that that would work out just fine as long as it doesn’t sit too long unbaked (overnight is okay)
I can not stand coconut. So my question to you is, does it taste like coconut at all? I usually use almond milk.
Nope, no coconut flavor here at all!
I see the one post that provides Macros and am concerned it lists so many carbs. Was that an accurate macro count for this recipe?
Hi! I just updated the nutrition for this – you can find all the stats right under the recipe. it’s an old recipe and I forgot to convert it! I based it on 10 servings and the carb count seems accurate to me, hope this helps.
Amazing! Made this today with a few alterations. Regular potato instead of sweet potato, mushrooms instead of brussel sprouts (sautéed after the onions) and added rosemary – so good!!!
Yum! How did the regular potato work out as a crust? I’ve been meaning to try it!
I didn’t want to commit to 12 eggs, so I hailed the recipe. Kicking myself now! It’s delicious, and I will be making it again. I skipped caramelizing the onions opting to roast them with the other veggies and omitted the bacon since I’m on the vegetarian Whole30 plan. Thank you!!
Can I use something instead of the coconut milk or just eave it out completely. I do not like the way it tastes
You can use another non-dairy milk or possibly just leave it out – it shouldn’t affect the final outcome much!
This is absolutely delicious!! I don’t always love egg casseroles because I don’t like if it’s too eggy. This is perfect! I used 1/2 cup nutritional yeast instead of 1/4 cup because we LOVE nutritional yeast and I didn’t salt any extra because I cooked in the bacon fat. This could be a meal for anytime of the day, not just breakfast!! It’s a little prep work, but worth every second. I buy already shredded Brussels and that’s a huge time saver. I almost never leave reviews on recipes, but this needed another praise for sure!!