This Paleo Breakfast Casserole is loaded with so many goodies and is perfect for brunch or to make ahead! Roasted sweet potatoes form the “crust” and are topped with crispy bacon, roasted brussels sprouts, caramelized onions, and baked with eggs. Nutritional yeast adds the right amount of “cheesy” flavor in this Whole30 friendly breakfast recipe.
Guys, I completely spoiled myself with this recipe. Not because of the bacon and caramelized onions (or at least, not entirely) and not because of the roasted sweet potatoes and Brussels sprouts (god I love them!)
But really, I spoiled myself mostly because I woke up for 3 days straight and DID NOT HAVE TO COOK BREAKFAST.
Let me tell ya, it was a glorious 3 days. Well, actually it wasn’t totally glorious because it happened to coincide with the annoying upper respiratory infection that arrived in time for my birthday.
Don’t even ask why I made 2 breakfast casseroles when I was sick and it was a challenge to just stand upright. The short answer is that I don’t take sick days, the honest answer is that I can’t resist an opportunity to challenge torture myself.
I definitely do not recommend you do the same! Wait until you’re good and healthy, then make 3 of these babies (or however many fit in your fridge/freezer) and go on a breakfast strike for a solid week.
So let’s get right into the details here! When I was planning this Paleo breakfast casserole, there were a few things I NEEDED to include.
Ingredients Needed for Paleo Breakfast Casserole
- Nitrate free bacon (Sugar free for Whole30)
- Sweet potatoes (peeled & sliced into thin rounds)
- Brussels sprouts (cut in quarters or chopped)
- Melted cooking fat
- Onion (sliced thin)
- Eggs
- Coconut milk
- Nutritional yeast
- Garlic powder
- Sea salt & black pepper
Caramelized onions and bacon, to start – there are simply no other ingredients that provide the flavor you get from that combo! I used my favorite sugar free bacon, discovered during my first Whole30, way back when, from U.S. Wellness Meats and my family swears it’s the best bacon they’ve had, Paleo or not. That’s big stuff around here!
Second, I wanted sweet potatoes. Because let’s face it – I need some carbs in my breakfast and I wanted this casserole to be all inclusive – no frying or roasting on the side allowed, period.
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 mushrooms, peppers, really anything roast-able. 🙂
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.
How to Assemble Paleo Breakfast Casserole
First, grease a casserole dish with coconut oil and line a baking sheet with parchment. Cut your bacon into one-inch pieces and cook them in a skillet until crisp. Drain the bacon and set aside but reserve the bacon fat for later.
Toss the sweet potato rounds in your cooking fat of choice and arrange them overlapping in the bottom of the casserole dish. Arrange the Brussels sprouts in a single layer on your prepared baking sheet. Place the sweet potatoes and Brussels sprouts in a 425 degree oven to roast. The sweet potatoes will take about 30 minutes and the Brussels sprouts will take 20 minutes.
Caramelize the onions in the reserved bacon fat over low-medium heat for about 25 minutes.
Lower your oven heat to 400 degrees. Over the sweet potatoes in the baking dish, layer the Brussels sprouts, caramelized onions, and bacon. Whisk the eggs, coconut milk, nutritional yeast, and spices in a separate bowl and pour the mixture over the veggies and bacon. Bake for 25 minutes until set and enjoy!
Ready to get started? We’re about to enter complete breakfast casserole bliss. Let’s go!
Paleo Breakfast Casserole {Whole30}
Paleo Breakfast Casserole {Whole30}

Ingredients
- 12 slices nitrate free bacon sugar free for Whole30
- 2 large sweet potatoes peeled and sliced into thin rounds approximately 1/4"
- 1 tbsp melted cooking fat** + sea salt for roasting the sweet potatoes
- 3 cups Brussels sprouts tops removed and either quartered or chopped, plus about 1 tbsp cooking fat** plus a pinch of sea salt for roasting
- 1 large onion or 2 small sliced thin
- 12 eggs
- 1/3 cup full fat coconut milk
- 1/2 tsp salt plus to suit your taste
- 1/4 cup nutritional yeast this is for a cheesy flavor, you can also sub Parmesan if you include dairy in your diet
- 1/2 tsp garlic powder
- Black pepper to taste
Instructions
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Preheat your oven to 425 F and grease a 9x13" casserole dish with coconut oil, and line a large baking sheet with parchment paper.
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Cut the bacon into 1" pieces and cook in a large heavy skillet, over medium high heat, stirring occasionally for even browning, until crisp. Remove with a slotted spoon to drain on paper towels and set aside. Reserve at least 3-4 tbsp of bacon fat to caramelize onions.*
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Next, roast the sweet potatoes and brussels sprouts. Toss the sweet potato rounds with cooking fat of choice and sea salt to taste (I add a generous pinch) and arrange, (overlapping since they will shrink after roasting) over the bottom of your casserole dish.
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Arrange the brussels sprouts on the parchment lined baking sheet in a single layer. Place the casserole dish and baking sheet in your oven to roast. The sweet potatoes will roast for about 30 minutes until soft and the brussels sprouts for about 20.
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Meanwhile, caramelize the onions. Heat the pan you cooked your bacon in over low/medium heat and add the onions, tossing with the leftover reserved bacon fat*
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Add a pinch of salt, and cook, stirring occasionally, adjusting the heat if any onions begin to brown too quickly. Cook the onions long and slow (about 25 minutes) to bring out the most flavor. Once the onions are deeply caramelized and very soft, remove from heat.
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While the onions cook, whisk together the eggs, coconut milk, nutritional yeast, salt, pepper, and garlic powder.
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Lower your oven heat to 400 F, then assemble the casserole. Layer your roasted brussels sprouts over your sweet potato rounds in the casserole dish. Remove the caramelized onions with a slotted spoon and layer over the brussels sprouts, follow with the cooked bacon. Finally, pour all the whisked egg mixture over the casserole to evenly cover.
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Bake in the 400 F oven for about 25 minutes until the center is just set and edges begin to turn light brown. Allow to cool for a bit in the baking dish before cutting into pieces and serving warm. Leftovers can be stored, covered, in the refrigerator for up to 5 days*** Enjoy!
Recipe Video
Recipe Notes
*If you want to use a different cooking fat to caramelize the onions, coconut oil or ghee are your best bets!
**Melted coconut oil, ghee, or light-flavored olive oil will work well here
***If you wish to freeze this casserole to make ahead of time, cover tightly and freeze before the final baking step.
Nutrition
What I Used to Make My Paleo Breakfast Casserole
Want more Whole30 and Paleo breakfast recipes? Try one of these!
Roasted Butternut Bacon and Apple Hash
Chorizo Sweet Potato Frittata with Caramelized Onions
Whole30 Breakfast Recipes on the Web:
Buffalo Chicken Breakfast Casserole
Breakfast Baked Sweet Potatoes with Almond Butter, Banana and Chia
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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?