Spaghetti Squash Egg Bites
If you’re a fan of the egg bites at Starbucks, this homemade copycat idea is for you. This egg bites recipe features healthy and hearty spaghetti squash and a hint of spice. They are an excellent meal-prep option that makes busy days much easier.
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Make ahead breakfasts like these egg muffins are the best. Other breakfasts you can prep in advance include these protein-packed peanut butter banana overnight oats or these almond flour blueberry muffins. Check out all of our healthy breakfast recipes for more inspiration.
Why you will love this recipe
- The egg bites freeze and reheat well, making them perfect for meal prep.
- This recipe is perfect for using leftover spaghetti squash.
- Naturally gluten-free and low in carbohydrates. Bonus!
Ingredient notes
Find the complete ingredient list, with measurements, in the recipe card below.
- Onion – Caramelized before going into the egg mixture, and they are SO good.
- Cooked Spaghetti Squash – A great way to use any leftovers. Check out this post on how to make spaghetti squash.
- Eggs – Choose local farm eggs if possible.
- Salsa – Pick your own spice level. We love Herdez in medium.
- Cheese – Great melty cheeses include cheddar and Parmesan.
- Olive Oil – For sautĂ©ing the onions and squash.
- Salt and Pepper – A pinch of sea salt and black pepper brings out the best flavors in your ingredients.
- Customers find these organic eggs to be the best they've bought, with great flavor.
Equipment
Knife and Cutting Board – This is for prepping the onions. We love our Victorinox chef’s knife that we’ve used for over 10 years.
Pan or Skillet – Use a large frying pan or skillet for cooking the onions.
Large Bowl – To stir everything together.
Muffin Tin – Well, egg bites muffin tin, makes sense, right? I use 8 wells of a regular-sized muffin pan for this recipe.
- Free of PTFE, PFOA, PFAS, lead, cadmium, and other toxic materials that can leach into your food.
- Can withstand oven temperatures up to 550ºF.
Instructions
Scroll to the recipe card at the bottom for the FULL recipe details.
Step 1
Start by preheating the oven and lining the muffin tin. This recipe makes 8 egg cups, so line 8 muffin cups.
Step 2
Caramelized onions are perfect in egg dishes, so the first order of business is to get the onions going.
Heat the olive oil over medium-low heat in a skillet, then add in the thinly sliced onions and season them with salt and pepper. Cook them, stirring every so often, until they are browned and caramelized.
Step 3
Once the onions are nice and caramelized, add the cooked spaghetti squash to the pan. Stir everything around and remove the pan from the heat.
Step 4
Next, in a mixing bowl, whisk together the eggs.
Since I like things on the spicier side, I incorporate some salsa into the mix. Salsa and eggs are a match made in heaven in my humble opinion.
Step 5
Mix everything together and pour it into the muffin tin.
Expert Tip!
Use a large measuring cup or container with a spout to pour the egg mixture into the muffin tin wells. It makes filling them cleaner and helps keep the portions even.
Step 6
A nice sprinkling of freshly grated Parmesan cheese, and these protein and veggie packed cups are ready for the oven.
Bake them for about 30 minutes, until the eggs are set, and enjoy warm.
Substitutions and recipe variations
Mix and match the veggies. Ideas include spinach, chopped bell peppers, tomatoes, and mushrooms.
Boost the protein by adding some cooked meat to the egg mixture before baking. Add cooked turkey, bacon, or ground beef, to name a few ideas. Try these tuna melt egg bites for a seafood twist.
Parmesan can be swapped for cheddar, mozzarella, feta, or goat cheese.
Serving suggestions
Plate with a side of salsa for an extra kick and add a lettuce salad and some homemade tater tots for a full on plate of deliciousness.
A hot cup of chai spiced coffee or a bulletproof coffee with MCT oil to supercharge that breakfast.
FAQS
Yes. They can be prepared ahead for breakfasts or lunches and reheated when needed.
That’s normal for egg-based dishes. They naturally puff as they bake and settle as they cool.
Storage tips
To Store: Store them in an airtight container in the refrigerator for up to 3 days. Reheat individual portions in the microwave or oven as needed.
To Freeze: Let them cool completely, then freeze in an airtight container or freezer-safe bag. Thaw in the refrigerator before reheating for the best texture.
More recipes with spaghetti squash
If you’ve tried this method for how to make egg bites, please give me a rating and let me know how it turned out by leaving me a comment below. I’m always interested in feedback!
*Originally posted February 19, 2014, updated June 15, 2019, and updated again August 20, 2026.*
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Egg Bites with Spaghetti Squash
Ingredients
- 1 tbsp olive oil
- 1 cup thinly sliced onions
- 2 cups cooked spaghetti squash *approximately ½ a medium cooked squash
- ¼ cup salsa
- 5 eggs
- ¼ cup freshly grated parmesan
- sea salt and pepper to taste
Instructions
- Preheat the oven to 350° and line a muffin tin with paper or silicone liners.
- Heat olive oil in a large skillet over medium-low heat. Once warm, add the thinly sliced onions and season with sea salt and fresh pepper. Cook the onions, stirring occasionally, until they are browned and caramelized, about 10 minutes.
- Stir in the spaghetti squash and mix well. Remove the pan from the heat and set aside.
- In a large bowl, whisk together the eggs, then stir in the salsa. Add the veggies to the mixture and stir again.
- Pour the mixture into your prepared muffin tin and top with grated cheese.
- Bake for 25-30 minutes, until the eggs are set.
Looks easy and I will try it!
Awesome! Thanks Regina. đŸ™‚