Butternut Squash Egg Muffins

Name: Butternut Squash Egg Muffins
Prep time: 15 min
Cook time: 75 min
Total time: 90 min
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)

These quick and easy Butternut Squash Egg Muffins are a great make-ahead breakfast option that freeze, travel, and reheat super 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!

This recipe is…
Why You’ll Love This Egg Cups Recipe
Baked Egg Cups Recipe Ingredients
Recipe Variations and Modifications
How to Make Egg Cups in the Oven
Egg Cups Recipe Tip
How to Serve Egg Muffins
How to Store and Reheat
Frequently Asked Questions
More Favorite Breakfast Recipes
Butternut Squash Egg Muffins Recipe

GFGluten Free PPaleo

Here at Fed & Fit, we love getting feedback from you, our readers. Recently, we noticed a lot of community requests for:

Make-ahead breakfasts
Travel-friendly breakfast ideas
EASY recipes
Freezer-friendly breakfast ideas

So we’re excited to share our Butternut Squash Egg Muffins – a baked egg cup recipe that ticks all these boxes — and takes just 15 minutes to prep 24 servings!

First, you roast some butternut squash. You can either use a whole butternut squash (like we did), OR you can make things easier (see request #3 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.

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 the squash.

Sprinkle the tops with crumbled pieces of bacon and bake until firm. Then, garnish with snipped chives or another green herb. Let them cool enough to handle and then enjoy right away. OR, save some for busy mornings down the road by stashing some in the freezer (more on that below).

Looking for more make-ahead breakfast recipes to help streamline hectic mornings? Try our Balanced Breakfast Egg Cups, Tiramisu Overnight Oats, Blueberry Sweet Potato Breakfast Meatballs, and Frozen Breakfast Sandwiches.

Why You’ll Love This Egg Cups Recipe

Just 15 minutes of prep!
Makes a big batch of 24 egg cups for eating now or freezing for later.
A great make-ahead breakfast to satisfy everyone in the house.
Bake once and have breakfast for the whole work week!
Travel-friendly

Baked Egg Cups Recipe Ingredients

Eggs, squash, bacon, butter, S&P…it’s everything you need to bake up a big batch of these egg muffin cups! Find ingredient notes (including substitutions and swaps) below.

Ingredients for butternut squash egg muffins sit in a variety of bowls and plates on a light grey surface.

Butternut squash – you’ll need a 2-3 pound butternut squash
Eggs – 18 whole eggs are the base of these breakfast cups
Salt – we season with 1/2 teaspoon salt…
Pepper – and black pepper to taste
Bacon – you’ll also need 8 slices of bacon
Butter – 2 tablespoons butter (or ghee) grease the muffin cups
Chives – garnish the cups with 2 tablespoons chives for garnish, if you’d like

A full ingredient list with exact amounts can be found in the recipe card below.

Recipe Variations and Modifications

Customize this recipe to your taste buds with a few easy suggestions:

Herbs – if you don’t have fresh chives on hand, swap in fresh or dried parsley, dill, basil, or cilantro.
Cheese – boost the flavor of these egg cups with a sprinkle of shredded parmesan, mozzarella, cheddar, or jack.
Spice – want to add a little heat? Add about 2 teaspoons of red pepper flakes to the egg along with the salt and black pepper.

How to Make Egg Cups in the Oven

Here’s how these quick and easy baked egg cups come together with just 15 minutes of prep!

Halved roasted butternut squash sits on a stainless steel tray on a light gray surface.

Eggs are whisked in a stainless steel bowl on a light gray surface.

Step 1: Cut a 2-3 pound butternut squash in half, scoop out seeds, place face down on a baking sheet and bake at 375°F for 45-60 minutes, until tender. Reduce heat to 350. Let squash cool for at least 15 minutes.

Step 2: While squash is baking, cook the bacon, then crumble.

Whisk eggs with salt and pepper until fully combined.

Roasted butternut squash pieces sit in a muffin tin on a light gray surface.

Crumbled bacon is placed on top of butternut squash egg mixture in a muffin tin on a light gray surface.

Step 3: 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.

Step 4: Fill each tin 3/4 of the way with the egg mixture. Top with bacon, equally dividing 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.

Egg Cups Recipe Tip

Squash shortcut – if you’d like to save a little time, you can use 2 pounds of pre-cut butternut squash and then puree it instead of buying a whole squash.

How to Serve Egg Muffins

Once the egg cups cool to the touch, pop them out of the muffin tins. Serve them warm, garnished with snipped chives.

How to Store and Reheat

Store the cooked egg cups in the refrigerator for up to 5 days. Reheat in the microwave, or in the oven on a baking sheet.

If you freeze the egg cups, you can have a few options when defrosting:

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 the lid. Let them cook for an additional 5 minutes, or until warmed through.

Frequently Asked Questions

How do you freeze egg cups?

If you want to stash these egg cups away in the freezer to eat later, we recommend wrapping packets of 2-3 muffins (about a serving size) in wax paper. Tape the packets closed, and place them in a gallon freezer bag. They’ll keep well for up to 3 months.

Why are my egg cups rubbery?

If your egg muffins are heavy and rubbery instead of light and fluffy, they’re likely overcooked. You may want to test the temperature of your oven to make sure it’s correctly calibrated. If it is, start checking your baked egg cups after 15 minutes and take them out of the oven when the centers are just set.

You’ll also want to take the egg cups out of the muffin tins as soon as they’re cool enough to handle, and move them off the stovetop so they won’t continue to cook with carryover heat.

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