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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ohmygoodness. This looks AMAZING. I will be making a few of these next weekend. YUMMY!!
I made this today. It is incredibly tasty! Thank you!
Awesome!
What is the approximate calories for each serving?
Yes I would like to know the nutritional information for this!!!
Courtesy of Spark people macros approximate based on skin on sweet potato and 10 slices of thick cut bacon, all else is according to the recipe.
Nutrition Facts
8 Servings
Amount Per Serving
Calories 363.6
Total Fat 17.7 g
Saturated Fat 3.2 g
Polyunsaturated Fat 1.6 g
Monounsaturated Fat 5.2 g
Cholesterol 10.9 mg
Sodium 409.7 mg
Potassium 116.4 mg
Total Carbohydrate 32.0 g
Dietary Fiber 7.1 g
Sugars 10.2 g
Protein 20.2 g
Vitamin A 297.4 %
Vitamin B-12 27.1 %
Vitamin B-6 93.3 %
Vitamin C 24.8 %
Vitamin D 1.0 %
Vitamin E 0.0 %
Calcium 4.8 %
Copper 1.3 %
Folate 0.0 %
Iron 3.6 %
Magnesium 1.0 %
Manganese 1.0 %
Niacin 61.7 %
Pantothenic Acid 1.7 %
Phosphorus 3.3 %
Riboflavin 120.0 %
Selenium 6.7 %
Thiamin 136.7 %
Zinc 4.2 %
*Percent Daily Values are based on a 2,000 calorie diet.
Omg Michelle! This recipe is amazing. I never comment on blogs but I have to for this one. I just made it with the intention to put it away for tomorrow and the remainder of next week cornmeal prep but I had to have a piece it looks and smells so good! Tastes amazing too. Thanks!
This is definitely a favorite! Thrilled you liked it!
This is so delicious! I added red peppers and spinach the last 5 minutes of carmelizing the onions and they tasted great. This is converting friends and family members to paleo. They all thought paleo was just boring food before.
Sounds so good! Glad you enjoyed!
How would this be without bacon for vegetarians?
So I made this today and to be honest while I was making it, I was thinking this will be the first and last time because it’s just too much work when you have a full time job. However, after one taste, I knew I was going to be making it again and again. I just have to figure out a strategy for making it quicker. One thing I”ll do is cut up vegetables for 2 complete recipes. Or maybe just make 2 and freeze one. But it is really delicious!
LOL because I totally agree 🙂 It’s definitely time consuming to make if you do all the steps at once – for recipes like this I will chop everything ahead of time and then make it on a Sunday while I’m home doing other things. If you can swing making 3 at once and freezing two that would be awesome!
Hi Michele,
I made three! Cooked one and froze two. how much longer should the frozen one be cooked?
Hi! Not sure…I’d say watch it until everything is set 🙂 Hope you enjoy!
I actually very rarely make breakfast in advance since I have oats most mornings, but if I had a family? Omg a huge dish like this would be a blessing. And isn’t nutritional yeast the best?! You’re right about it adding a certain “something”
Made-ahead breakfasts are a life saver for the working running mom that I am! I love mushrooms onions and cauliflower with my eggs. Sweet potatoes are also a must when I run before work. This casserole looks delicious! I will try it for sure.
When I clear out my fridge a little, I need to make this! With sooo much good stuff, I’m pretty sure I’d eat it at least two meals a day.
Has anyone calculated the calories in this dish ? It looks delicious!
Do you recommend freezing this with the egg added or without? I was thinking about freezing just the veggies and bacon, then adding the egg the day I cook it.
I think that makes more sense so you’re not dealing with anything raw. So, make the veggies and bacon and then whisk together the egg mixture the day of. Hope you like it!
I made this for Christmas breakfast. It was delicious! Even the people who are not following Whole 30 loved it. I cooked all the veggies the day before, then assembled it in the morning, and popped it in the oven. It turned out perfectly baked, very filling, and yummy. Next time I will bake with fewer onions and more bacon, just because we love bacon.
That’s incredible! Thanks for letting me know – I love getting comments like this!
And I thought I”d put in more onions. I love carmalized onions in my food!
It is very rare that I don’t have to adjust spices in recipes to my liking but this was amazing! Definitely time consuming but totally worth it. Cooking the onions in the bacon fat was such a nice touch. Can’t wait to make this again!
Oh I am the same with spices! So happy you liked this! I also wish it took less time to make but then again, at least it makes a lot 🙂
I did the prep work last night and then added the egg mixture and baked this morning. It is beautiful and yummy. My 11-year-old son even ate it for breakfast. That is something I consider a hit! Thanks for the recipe!
Definitely a hit if an 11 year old is on board! Go you for getting it all ready the night before!
How long will this keep? 3Days?
it should keep 5 days in the fridge 🙂
This casserole is amazing!! Usually I am someone who changes recipes to what I think would be great, but this recipe looked so satisfying that I didn’t change anything and it was sooo perfect and delicious! My husband immediately asked for it to be brought into our meal rotation and my toddler licked his plate clean 🙂 Bravo on the delicious recipe!
So happy to hear you guys loved it! Especially because it DOES take some work, it’s always nice to have the payoff in the end!