Healthy Breakfast Casserole

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This Healthy Breakfast Casserole is the perfect addition to a holiday brunch, and has a sneaky serving of veggies inside. You’d never know just by tasting it!

slice of breakfast casserole served on plate.

Why You’ll Love It

There are sneaky veggies inside. You can fit 3 pounds of cooked spaghetti squash in this recipe, but the yellow color blends right in with the eggs. It helps to bulk up the casserole, without an overpowering veggie flavor. In fact, I served this at Easter and my family members preferred it over a regular Quiche Lorraine! (It’s naturally gluten-free, too.)

It’s loaded with protein and fiber. Thanks to the protein-rich eggs and fiber-rich spaghetti squash, this egg casserole should leave you feeling full for hours. It’s perfect for those following a low-carb eating plan, or a paleo plan that allows for some cheese.

You can make it vegetarian. Swap the bacon in this recipe for crispy mushroom bacon, instead. If you haven’t tried mushroom bacon yet, your mind will be blown once you taste it.

You can prep ahead of time. I always cook the spaghetti squash the day before I plan on making this, because it can be a bit time consuming. I have tutorials on how to cook spaghetti squash in the oven and in the Instant Pot, if you want to plan ahead of time. You can cook the bacon ahead of time, too!

It’s flexible. Want to use a different cheese or mix in? Like most breakfast casserole recipes, this one lends itself to all sorts of modifications. I imagine you could use frozen shredded hash browns or roasted sweet potatoes to replace the spaghetti squash, and you can use cooked turkey sausage, ground turkey or beef, mushrooms, or bell peppers to replace the bacon, if you prefer.

It’s perfect for meal prep. Bake this savory breakfast casserole over the weekend, then store the slices in the fridge for an easy grab-and-go breakfast. It should keep well for at least  5 days.

How to Make a Healthy Breakfast Casserole

1. Prep the ingredients.

You’ll need to cook the spaghetti squash and bacon ahead of time, so preheat your oven to 400ºF. Since the squash takes the longest to cook, start with that.

Cut the squash in half cross-wise, meaning you’ll cut through only the center of the squash where it’s the most hollow. (This is the easiest way to cut a spaghetti squash, in my opinion.)

Use a spoon to remove the seeds, then place the halves cut-side-down on a rimmed baking sheet lined with parchment paper. Bake at 400ºF until the squash is tender, about 45 to 60 minutes.

Now that the squash is cooking, line another large rimmed baking sheet with parchment paper, so you can prep the bacon. (Oven cooked bacon is the easiest, in my opinion, but you can also prepare Air Fryer Bacon, if you prefer.)

Arrange the bacon in a single layer on the bacon sheet, avoiding any overlap for the crispiest results. Cook the bacon at 400ºF for 20 to 25 minutes, or until it looks crispy. You can do this while the spaghetti squash is cooking, to maximize your time.

The last thing to prep is the onion. Add a tablespoon of olive oil to a large skillet over medium heat, and sauté the onion until it’s soft and translucent, about 5 to 8 minutes. Set it aside to cool.

Note: All of this can be done a day or two in advance, if you are planning a big holiday brunch. I never cook the squash and bacon on the same day, because I don’t like to spend more than an hour in the kitchen on a single meal!

cooked breakfast casserole ingredients.

2. Mix. 

Let the cooked ingredients cool slightly, so they are comfortable to work with (no burning your hands!) and won’t start to cook the eggs when you mix them together later.

Use a fork to scrape the spaghetti squash strands into a large mixing bowl. You should get about 3 to 4 cups of cooked squash from a 3-pound spaghetti squash. Crumble the bacon between your fingers and add that to the bowl, along with the sautéed onions. (Save a few bacon pieces to sprinkle over the top, if you’d like to.)

Crack the eggs into a separate bowl, just to make sure you can scoop any broken egg shells out easily. Mix in the salt and pepper, and stir well.

Pour the egg mixture into the large bowl of veggies and add in half of the grated gruyere cheese. Mix well, then pour the mixture into a greased baking dish. (I use a 9-inch by 13-inch baking dish.)

breakfast casserole ingredients mixed together and in pan.

3. Bake. 

Sprinkle the remaining cheese and any reserved bacon pieces over the top, then bake at 400ºF for 40 to 45 minutes, or until the top looks golden and the center of the breakfast casserole has puffed up in the center.

Remove the pan from the oven and let it cool for 15 to 20 minutes, before slicing and serving. I like to sprinkle a few chopped chives over the top, for a pop of color.

Leftovers can be stored in an airtight container in the fridge for up to 5 days. It’s such an easy breakfast to reheat throughout the week!

Need to make a swap? If you don’t care for gruyere cheese, you can use cheddar cheese or even feta cheese instead.

breakfast casserole before and after baking

Make-Ahead Tips

Want an easy make ahead breakfast casserole? Here are some tips.

1. Prep the squash. You can bake a spaghetti squash up to 4 days in advance, and keep it stored in the fridge until you’re ready to use it.

2. Cook the bacon & onions. You can cook these both up to 4 days in advance, too! They are easy to mix into the casserole when you’re ready to cook it.

3. Assemble and store overnight. If you don’t want to mix everything together in the morning (even with the prep above done), you can assemble this un-baked casserole the night before and keep it tightly covered in the fridge for up to 24 hours.

When you’re ready to cook it, place the cold casserole dish into a cold oven. Preheat the oven to 400ºF and set the timer for 45 minutes. The casserole may need an additional 10 to 15 minutes of cook time since you’re starting with the cold temperature, but you don’t want to risk putting a cold casserole dish into a HOT oven, and having it shatter from the temperature difference! So, just check on it after 45 minutes, and if the center hasn’t puffed up yet, give it another 10 minutes or so to finish cooking.

breakfast casserole sliced and served with spatula.

breakfast casserole sliced and served with spatula.
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5 from 2 votes

Healthy Breakfast Casserole

This healthy breakfast casserole is loaded with protein and veggies, with a sneaky vegetable hiding inside. It reminds me of Quiche Lorraine without a crust!
Course Breakfast
Cuisine American
Keyword healthy breakfast casserole
Prep Time 1 hour
Cook Time 45 minutes
Total Time 1 hour 45 minutes
Servings 12
Calories 248kcal


  • 1 (3-pound) spaghetti squash
  • 12 ounces thick-cut bacon
  • 1 tablespoon olive oil
  • 1 medium yellow onion , chopped
  • 8 whole eggs
  • 5 ounces Gruyere cheese , shredded and divided
  • 1 teaspoon fine sea salt
  • 1/2 teaspoon black pepper


  • Preheat your oven to 400ºF and line two large rimmed baking sheets with parchment paper. Cut the spaghetti squash in half crosswise (so you only cut through the hollow middle-- easier!) and scoop out the seeds with a spoon. Place the squash cut-side-down on the pan, and bake until tender, about 46 to 60 minutes.
  • To cook the bacon, arrange the strips in a single layer, without overlap, on the other lined baking sheet. (Make sure it has a rim, to catch the grease as it cooks.) Place it in the same oven as the squash and let it cook until crisp, about 20 to 25 minutes. It will crisp up even more as it cools.
  • Once everything is in the oven, add the olive oil to a large skillet over medium heat and sauté the onion until it is soft and translucent, about 5 to 8 minutes. Set it aside to cool while everything else finishes cooking.
  • Let the spaghetti squash and bacon cool, until they are comfortable enough to handle. (You don't want to mix the eggs into piping hot squash, or they will scramble as you stir. This is why I recommend cooking the squash and bacon the night before you want to assemble this casserole, so you don't have as much prep time in a single day.) Once you can handle the squash, use a fork to scrape the spaghetti squash strands into a large mixing bowl. Crumble the bacon in to pieces, and sprinkle them into the bowl, too. (Reserve a few bacon pieces to sprinkle on top, if you like.)
  • Crack the eggs into a separate bowl (just in case you need to fish out broken egg shells later) and season with the salt and pepper. Whisk well with a fork, then pour it into the mixing bowl, along with the onions, and half of the grated cheese. Stir well.
  • Grease a 9" by 13" baking dish with spray oil, then pour the mixture into the pan. Sprinkle the remaining cheese over the top, along with any reserved bacon pieces. Bake until the top is golden and has puffed up, about 40 to 45 minutes at 400ºF.
  • When the breakfast casserole is done cooking, remove it from the oven and let it cool for 10 to 15 minutes. Slice it into 12 squares and serve warm, with a few freshly chopped chives on top, if desired. Leftovers can be stored in an airtight container in the fridge for up to 5 days.


Nutrition information is for 1 of 12 slices. This information is automatically calculated, and is just an estimate, not a guarantee.
For make-ahead tips, be sure to read the full post above! 


Calories: 248kcal | Carbohydrates: 7g | Protein: 11g | Fat: 19g | Saturated Fat: 7g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 8g | Cholesterol: 141mg | Sodium: 522mg | Potassium: 208mg | Fiber: 1g | Sugar: 3g | Vitamin A: 378IU | Vitamin C: 2mg | Calcium: 158mg | Iron: 1mg

If you try this breakfast casserole recipe, please leave a comment and star rating below letting me know how you like it!

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Thanks again for sharing this recipe!


This looks and sounds delicious! I bet it would be really good with an addition of sun dried tomatoes, too! Thanks for posting recipes so often! I can’t make them fast enough :0).


I made this last night it is delicious and it came together easy. I am looking forward to trying it with different meants and cheeses in the future.


Hello! Just came across your blog and bookmarked this recipe for the weekend. However, it has since disappeared from Against All Grain’s site. Can you pls help?


    How strange! I’ll try to get the recipe up sometime soon. 🙂


It is missing…and my squash is cooked at waiting!!! Please post!


    It’s up! Hope you enjoy it. 🙂


      It must have gone back down. is saying this when I click on the link you’d originally had up on this recipe:
      “Not Found, Error 404
      The page you are looking for no longer exists.”
      Thank you for posting all of the details to the recipe here, though. I hope to make this, soon!


(Full instructions to cook spaghetti squash are posted here.) -> the link is broken


Hi Megan, I’m a little confused. I thought spaghetti squash is considered a starch under the winter squash category. Would this be properly combined w/ eggs, cheese and bacon? or is spaghetti squash considered a non-starchy veggie?


I’m a teen and I am trying to come with healthy ideas to take to school for lunches and snacks. Any suggestions? Thanks!

Marcia Burcham

Can I make this ahead of time and bake after two days or should I bake and reheat?


Hi Megan,
Can this be made ahead of time and frozen? If so, do any modifications need to be made and what would be the best way to reheat it?
I love your site and have told so many people about how wonderful you and your recipes are! Thanks!


I absolutely love making this casserole for breakfast! So yummy!!


Yum! I’ll make this with salmon bacon instead since I don’t eat pork and I can already tell it will be delicious! Thanks!

    Melissa B

    I had an abundance of eggs on hand and a spaghetti squash that I needed to use. Added mushrooms and subbed applegate chicken maple sausage for the bacon. It is so delicious, paired with a salad for an afternoon meal! Wrapped some individual portions for meals later in the week. So good!!


Looks amazing. Can’t wait to try it!

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