100-Calorie Cheese, Vegetable and Egg Muffins


This post may contain affiliate links.

Healthy Egg Muffins — Portable baked egg muffin cups that you can enjoy without worry! These healthy egg muffins are stuffed with protein, veggies, and cheese. The best kind of breakfast! Or snack. Or dinner.

100-Calorie Cheese, Vegetable and Egg Muffins

Make-Ahead Egg Muffins Recipe

I thought these egg breakfast muffins would be a good way to sneak in a few extra servings of vegetables and protein for my family. I was right. These muffins are a big hit, and bonus: they’re naturally gluten-free and vegetarian! 

I found myself grabbing one of these egg muffins here and there. And here and there. Before a workout, after a workout, with dinner, for breakfast, in school lunches. We took down the dozen of these in a day.

The egg muffins are soft, yet dense and chewy. I love the texture the vegetables add and I like the surprise of biting into a juicy pea or a crispy pepper piece!

Stack of Healthy Egg Muffins stuffed with veggies and cheese

Ingredients in Healthy Egg Muffins

To make egg muffins in the oven, you’ll need the following ingredients:

  • Shredded carrots
  • Orange bell pepper
  • Frozen peas
  • Frozen corn
  • Eggs
  • Salt and pepper
  • Shredded cheese 

Note: Scroll down to the recipe card section of the post for the ingredients with amounts included and for more complete directions.

Egg muffins with cheese and veggies

How to Make Baked Egg Muffins

These egg muffin cups couldn’t be simpler to prepare! Here are the basic recipe steps:

  1. Liberally spray a non-stick muffin pan with baking spray.
  2. Then, toss together the veggies in a mixing bowl and fill each muffin cup 3/4 full with the mixture.
  3. Crack the eggs into a measuring cup, season with salt and pepper, and whisk with a fork until smooth. Divide the eggs evenly between the 12 muffin cups.
  4. Sprinkle with your shredded cheese of choice, then bake.

Baking Tip

These egg muffins need to bake until the muffins are set, cooked through, and are lightly golden. Note that they will puff in the oven, but sink upon cooling. 

Baked egg muffins out of the oven

Make-Ahead Instructions

Make-ahead egg muffins are the perfect way to meal prep for the week ahead!

You can make a whole batch of these in advance and keep them for up to about a week in the fridge and then just reheat them in the microwave for 15 to 30 seconds. Makes a quick on-the-go snack!

However, I actually like them cold. (But I also love cold pizza, so do what sounds good to you.)

If you want to freeze the egg muffins, I recommend letting them cool completely to room temperature before flash freezing on a parchment paper-lined baking tray. The muffins should harden within 1 hour and can then be sealed in a freezer bag without fear of them getting squished or sticking together.

For best results, reheat egg muffins from frozen. If you thaw them first, the vegetables will weep and the eggs will become soggy. No, thank you!

Healthy egg muffins refrigerate for a quick snack

Recipe FAQs

Can I Add Other Veggies to These Egg Muffins?

Definitely! I used shredded carrots, orange peppers, frozen peas and corn, but you can use almost any veggie you like. It’s the perfect produce drawer clean-out recipe.

Rather than the shredded carrots, which serve to really bulk up the vegetable mixture, you could grate or dice leftover potatoes or sweet potatoes. Or work in some broccoli, asparagus, spinach, kale — whatever is seasonal or lurking in the bottom of your produce drawer and needs to get used, stat.

Can I add bacon, ham, or sausage to the muffins?

Yes, but you MUST cook bacon and sausage in a skillet before adding to the muffin cups. The egg muffins aren’t baked for long enough to cook raw bacon and sausage, plus all the veggies and egg.

Can I Use Egg Whites or Liquid Egg Replacer?

I’ve only made these baked egg muffins with whole eggs, although you could likely use liquid eggs or just whites. If you use one of these egg alternatives and this recipe turns out well for you, please let me know in a comment below! 

Can I Make Mini Egg Muffins? 

I used a regular muffin pan to make this egg muffin recipe, but you’re welcome to make mini egg muffins if desired. Just note that the bake time will be significantly reduced. 

Why are my egg muffins soggy?

Baked egg muffins can turn out soggy if too much liquid is added to them, or if the vegetables release a lot of liquid. To keep this recipe super simple, I didn’t saute the vegetables for this recipe (which a lot of egg muffin recipes have you do). However, I also didn’t add any liquid, such as milk, to the egg mixture. So, you shouldn’t have any issues with soggy egg muffins if you follow my recipe as written!

Can I Freeze Egg Muffins? 

Yes! This recipe is fabulous as make-ahead egg muffins. Flash freeze on a parchment paper-lined baking tray until firm, then seal in a freezer bag and reheat (from frozen!) in the microwave for about 30 seconds. 

Baked egg muffins for anytime

Tips for Making Healthy Egg Muffins

Non-stick spray: When making these egg bake muffins, you MUST spray the heck out of your muffin pan with non-stick spray. Then, run your finger through the spray and around the sides of the cups because every inch must be liberally coated with spray. If you miss a spot, you’ll be chiseling off stuck food with a knife. I speak from lots of experience.

Carrots: If using shredded carrots in this baked egg muffins recipe, I highly recommend shredding the carrots yourself as opposed to buying bagged shredded carrots. I find bagged shredded carrots to be too big, coarse, and tough due to the preservatives added.

Cheese: I topped the muffins with shredded mozzarella for extra flavor, richness, and it helps the muffins brown nicely on top. Use your favorite cheese. Or, if you’re trying to be good, omit it.

Recipe Video Tutorial

Pin This Recipe

Enjoy AverieCooks.com Without Ads! 🆕
Go Ad Free

4.51 from 51 votes

100-Calorie Cheese, Vegetable and Egg Muffins

By Averie Sunshine
100-calorie, portable, baked egg muffins that you can enjoy without worry! These healthy egg muffins are stuffed with protein, veggies, and cheese. The best kind of breakfast! Or snack. Or dinner.
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Servings: 12
Save this recipe to your email
Enter your email and we’ll send it to you!
Please enable JavaScript in your browser to complete this form.


  • 1 ½ cups shredded carrots, from about 4 medium peeled and trimmed carrots*
  • ½ cup small diced orange bell peppers
  • ½ cup frozen peas, I didn’t thaw
  • ½ cup frozen corn, I didn’t thaw
  • 8 large eggs
  • salt and pepper, to taste
  • 12 tablespoons shredded cheese, divided (I used Mozzarella)


  • Preheat oven to 375F. Spray a Non-Stick 12-Cup Regular Muffin Pan extremely well with cooking spray. Spray the base of the cavities and sides, then run your finger over the sides so that every inch is liberally coated with spray or you will be chiseling off stuck food; set pan aside.
  • In a large bowl add carrots, peppers, peas, corn (or mix and match with your favorite vegetables; read blog post for suggestions) and toss to combine.
  • Loosely pile about 3 tablespoons of vegetable mixture to each muffin cavity, or enough so that each is filled to about 2/3 to 3/4 full; equally distribute filling mixture among cavities until gone; set pan aside.
  • In a 2-cup glass measuring cup (the measuring cup makes for easy pouring), crack the eggs and lightly beat with a whisk.
  • Add the salt and pepper, to taste, and whisk to combine.
  • Pour about 2-3 tablespoons of egg into each cavity, equally distributing among the cavities. They will be about 3/4 full after being topped off with egg.
  • Top each cup with a generous pinch of cheese, about 1 tablespoon each.
  • Bake for about 18 to 20 minutes, or until muffins are set, cooked through, and are lightly golden. They will puff in the oven, but sink upon cooling.
  • Allow muffins to cool in pan on top of a wire rack for about 10 minutes before removing. You will likely need to rim each cavity with a small knife to help dislodge muffins. I find it easiest to rim with a knife and then ‘pop’ the muffin out using a small spoon.


  • *I recommend shredding the carrots yourself as opposed to buying bagged shredded carrots which I find to be too big, coarse, and tough due to the preservatives added.
  • Muffins will keep airtight for up to 1 week in the fridge; reheat gently in the microwave or serve cold.


Serving: 1, Calories: 100kcal, Carbohydrates: 6g, Protein: 7g, Fat: 6g, Saturated Fat: 2g, Polyunsaturated Fat: 3g, Cholesterol: 131mg, Sodium: 133mg, Fiber: 1g, Sugar: 2g

Nutrition information is automatically calculated, so should only be used as an approximation.

More Egg Breakfast Recipes: 

100-Calorie Cheesy Sausage and Egg Muffins — Low-carb baked egg muffins that are loaded with juicy sausage and cheese! EASY, ready in 30 minutes, and perfect for breakfast, brunches, snacks, or breakfast-for-dinner! You’ll want to keep a stash on hand!!

Asparagus, Peas, and Smoked Gouda Frittata — Even the pickiest eaters will eat green vegetables in this healthy & easy 25 minute recipe!

Asparagus, Peas, and Smoked Gouda Frittata - Even the pickiest eaters will eat green vegetables in this healthy & easy 25 minute recipe!

Egg-in-a-Hole Avocado Toast — Slathering warm egg in a hole toast with a creamy chive and lime-scented avocado spread is beyond DELICIOUS!! This avocado toast with egg is EASY, ready in 15 minutes, and perfect ANYTIME!!

Egg-in-a-Hole Avocado Toast

White Cheddar and Dijon Baked Eggs — Serve with toast or a salad for lunch or brinner, or with French toast or pancakes for breakfast. Cozy, comforting, and almost no dishes! 

White Cheddar and Dijon Baked Eggs - Fast & easy comfort food that's ready in 15 minutes! The Dijon & cheese just jazz these eggs right up!

Kale and Tomato Frittata — This frittata is healthy and I love the texture contrast between the tender eggs, chewy kale, and juicy tomatoes in this frittata.

Kale and Tomato Frittata

Cheesy Chicken, Broccoli, and Egg Skillet – A healthy-ish brunch, lunch, or breakfast-for-dinner recipe that combines juicy chicken, crisp-tender broccoli, eggs, and melted cheese!! EASY and ready in 30 minutes!!

Shakshuka with Italian Sausage — Shakshuka (aka Eggs in Hell) is an easy dish made of eggs poached in a spicy tomato sauce. It’s so simple to make and can be prepped for breakfast, brunch, or dinner! 

Eggs In Hell with Italian Sausage - Sometimes called Eggs in Purgatory or shakshuka, this easy dish includes eggs poached in tomatoes with sausage and garlic for tons of FLAVOR!! Perfect for breakfast, brunch, or breakfast-for-dinner!!
4.51 from 51 votes (41 ratings without comment)

Leave a Comment

Please note: I have only made the recipe as written, and cannot give advice or predict what will happen if you change something. If you have a question regarding changing, altering, or making substitutions to the recipe, please check out the FAQ page for more info.

Recipe Rating


    1. Thanks for the 5 star review, Sheenagh, and I am glad these are delish, versatile, and an A++ for you!

  1. 5 stars
    I did this with egg whites and bacon and one batch with sausage. you don’t really even need to spray with oil with the greasy meats in there.

  2. 5 stars
    I did this with egg whites and bacon and one batch with sausage. you don’t really even need to spray with oil with the greasy meats in there.

    1. Thanks for the 5 star review and glad that the work well for you. I do recommend spaying the tin if someone isn’t using greasier meats and/or doesn’t fully trust their muffin pan. Sometimes they do stick and with egg…it can be like cement if it does!