These Paleo Butternut Squash Egg Muffins are a great make-ahead breakfast option that freezes, travels, and reheats really well.

These butternut squash egg muffins are the perfect freezable, make-ahead breakfast for the week! The perfect combo of sweetness from the squash and salt from the bacon, these portable breakfast are also gluten free, Paleo, and Whole 30 friendly!

Writing recipes for the blog often feels like I’m solving a riddle. I start with a list of needs (or a collection of requests from YOU) and then start my experimentation on solutions! The needs that resulted in today’s recipe included:

  • Requests for make-ahead breakfasts
  • Requests for something EASY
  • Requests for a freezer-friendly breakfast
  • Requests for a breakfast with a starch
  • Requests for a travel-friendly breakfast

PHEW, that’s quite a list …but I’m not the kind of girl that backs away from a challenge. We got to work!

We finally settled on this little gem of a recipe, the Butternut Squash Egg Muffin! The concept is simple. First, roast some butternut squash. For this step, you can either use a whole butternut squash (like we did) OR you can make things easier (see request #2 above) by roasting pre-cubed fresh or frozen squash. We’re not looking for any special texture on the roasted squash, just that it’s cooked through. From here, it’s a downhill ride. Let the squash cool enough to handle (meaning, you can touch it without burning a finger), and then scoop it into greased (or parchment-lined) muffin tins. Whisk about 18 eggs (or less, if you’re making a smaller batch) with salt and pepper, and pour the whisked eggs over top the butternut squash.

Sprinkle the tops with crumbled pieces of bacon and bake until firm. Let them cool enough to handle and then enjoy right away. OR, if you’re wanting to stash these Butternut Squash Egg Muffins away in the freezer, I recommend wrapping 2-3 muffins (about a serving size) in wax paper, taping the package closed, and placing in a gallon freezer bag that you’ve labeled.

These butternut squash egg muffins are the perfect freezable, make-ahead breakfast for the week! The perfect combo of sweetness from the squash and salt from the bacon, these portable breakfast are also gluten free, Paleo, and Whole 30 friendly!
These butternut squash egg muffins are the perfect freezable, make-ahead breakfast for the week! The perfect combo of sweetness from the squash and salt from the bacon, these portable breakfast are also gluten free, Paleo, and Whole 30 friendly!

To defrost, you can either:

  • Oven method: place the frozen muffins on a baking sheet, spread out as much as possible. Place in a *cool* oven and turn oven on to heat to 350 F. Once at temperature, cook for an additional 5 minutes, or until warmed through. Note: if your oven is one that blasts HIGH heat to bring the box up to temperature, you’ll need to put the frozen egg muffins in once at temperature – baking for at least 10 minutes.
  • Microwave method: place the frozen egg muffins on a plate, cover with a paper towel, and microwave for 2-3 minutes, or until warmed through.
  • Stove method: place the frozen egg muffins in a skillet over medium heat and cover with a fitting lid. Once they’ve defrosted, remove lid. Let them cook for an additional 5 minutes, or until warmed through.

SO, let’s review our riddle. What breakfast recipe is…

  • Make-ahead friendly
  • EASY
  • Freezer-friendly
  • Balanced with a starch
  • Travel-friendly

…?

Butternut Squash Egg Muffins! BING, BANG, BOOM. I hope you love this recipe as much as we love solving riddles for you! You can also check out our Balanced Breakfast Egg Cups for another make ahead friendly breakfast option!

These butternut squash egg cups are the perfect freezable, make-ahead breakfast for the week! The perfect combo of sweetness from the squash and salt from the bacon, these portable breakfast are also gluten free, Paleo, and Whole 30 friendly!

Butternut Squash Egg Muffins

3.75 — Votes 12 votes
By Cassy Joy Garcia
Prep: 15 minutes
Cook: 1 hour 15 minutes
Total: 1 hour 30 minutes
Servings: 24 Servings
These Paleo Butternut Squash Egg Muffins are a great make-ahead breakfast option that freezes, travels, and reheats really well.

Ingredients  

  • 1, 2-3 pound butternut squash*
  • 18 eggs
  • 1/2 teaspoon salt
  • pepper to taste
  • 8 slices bacon cooked and crumbled
  • 2 tablespoons butter or ghee
  • 2 tablespoons chives for garnish

Instructions 

  • Preheat the oven to 375°F.
  • Cut a 2-3 pound butternut squash in half, scoop out seeds, place face down on a baking sheet and bake for 45-60 minutes, until tender. Reduce heat to 350. Let squash cool for at least 15 minutes.
  • While squash is baking, cook bacon then crumble.
  • Whisk eggs with salt and pepper until fully combined.
  • Grease 24 muffin tins with spray oil, butter or ghee, then spoon out a large scoop of the squash and place it in each tin. Then, fill each tin 3/4 of the way with the egg mixture. Top with bacon, equally divided among the 24 egg cups.
  • Bake for 25-30 minutes, until center is firmed.
  • Let egg cups cool, then remove from from muffin tin and garnish with chives. Serve immediately or freeze for later use!

Recipe Notes

*May use frozen butternut squash puree, reheated, or roast 2 lbs pre-cut butternut squash and then puree instead of buying a whole squash.

Nutrition

Calories: 112kcal | Carbohydrates: 7g | Protein: 6g | Fat: 7g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.1g | Cholesterol: 130mg | Sodium: 154mg | Potassium: 261mg | Fiber: 1g | Sugar: 1g | Vitamin A: 6248IU | Vitamin C: 12mg | Calcium: 47mg | Iron: 1mg

Additional Info

Course: Breakfast
Cuisine: American
Servings: 24 Servings
Calories: 112
Keyword: egg muffin cups

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About the Author

Cassy Joy Garcia, NC

Cassy Joy Garcia, a New York Times best-selling author, of Cook Once Dinner Fix, Cook Once Eat All Week, and Fed and Fit as well as the creative force behind the popular food blog Fed & Fit.


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24 Comments

  1. 3 stars
    I really want to love this recipe, but it always comes out bland when I make it. 🙁 Also, work to get most of the water out of the butternut squash when making this recipe. Cheers.

    1. I’m so sorry about that, D! Thank you for the feedback!

  2. Looks delicious. Do you think you could substitute for a different type of squash? I have a bushel of acorn squash I need to use up.

    1. I just added the nutrition facts to the recipe card, Laura!

  3. 4 stars
    I made this for this week’s grab-and-go breakfast and love them. They are good on their own or doctored up as either my hubby or I prefer! The recipe gave me more than 24 muffins (maybe my butternut squash was too big….)so I finished the batter with a heart shaped cake tin! Thank you for sharing!

  4. What is the texture of this? I’m getting so tired of frittata or egg muffin texture and was hopeful maybe adding butternut squash might make it less eggy?

    1. Silicone. Note that if they’re more likely to stick if still warm.

  5. Hello Cassy dear! Met with a potential GF Pastry Chef last week for Sara’s wedding cake and he was SO impressed that I knew you! So I was contemplating making this as a large quiche-type quick breakfast next week after we get home from Turkey Day 5K! Do you think it could be poured into a 9×13 dish and baked ahead and then reheated? And if I don’t have a blender, could I just use a hand mixer or should I do the food processor?

    1. I think it could work!! I’d bake it a little longer, just to be sure that it’s cooked-through. Also yes, food processor would work great.

  6. Hello again! This was a wonderful, tasty breakfast option for me- I made it for breakfast this week. I ran in to a small problem, which has happened before when I’ve made egg “muffins” – the eggs cups stick like crazy to the muffin tin! I tried to add extra oil to the pans to preemptively prevent this but to no avail. In the past I’ve used parchment paper cups, but had mixed results of egg sticking. Any suggestions?

    1. Hi Clare! If your muffin tin is metal, it will absolutely stick. If it’s silicone and still sticking, I recommend greasing thoroughly and, if they’re still sticking, try cooking a bit longer and then letting them cool *completely* before removing from the pan. Unfortunately, they’re just a sticky-prone food. I hope that helps some!

  7. How long will they keep fresh in the fridge and how long to keep in the freezer, if needed?

    Also, as with several of your other recipes, to freeze these egg cups, should they cool for about 30 min after baking and then put in freezer?

    Love your recipes & blog! You are so fun to follow!

    1. I would give them about 5 days in the fridge and no longer than 5 months in the freezer. Yes, let them cool first before freezing 🙂

  8. These are the best! Perfect way to get an extra serving of veggies in for my kiddos and the morning, so great to have ready for early and busy mornings AND they taste delicious. Thank you for this recipe!

  9. I can’t wait to try these! I think my kiddo will especially enjoy them. I was curious as to how much puree I should expect from the butternut squash? I noticed canned organic squash at my local grocery store and I was thinking about substituting it when pressed for time.

    Thank you!

  10. I’m going to make these this weekend!! I’ve got an Instant Pot (LOVE) so I’m going to do the squash in there:

    Cut butternut squash in half, scoop out the seeds, and place in Instant Pot, on trivet, with 1 cup water in the bottom. Set to Steam for 12 minutes and wait a few minutes before quick release.