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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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!!