Egg Muffin Cups

Free: Healthy Freezer Meals Recipe Ebook

Get It Now

This post may contain affiliate links, which help keep this content free. (Full disclosure)

One batch of this egg muffins recipe and you’ll never want to live without them in your fridge again! Sometimes called breakfast egg muffins, egg muffin cups or mini frittatas, they make a great meal prep low carb breakfast for busy days — whether your rushing out the door or rushing to get to your computer like me. Pair them with some bulletproof coffee for a filling, protein-packed morning meal.

This easy egg muffin recipe is made in a muffin tin with veggies, eggs, milk of choice, and cheese. I also have 15 variations and a rule of thumb for the ratios below, so you can customize it to your heart’s content.

If you prefer the yolks and whites separate, try oven baked eggs (also made in a muffin tin!) or cloud eggs instead.

Ingredients & Substitutions

This section explains how to choose the best ingredients for egg muffin recipes, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.

• Vegetables – I used broccoli, cauliflower, and bell peppers. Make it your own by choosing your favorite low carb vegetables, or simply use what you have in your fridge right now! Notes on the veggies:
  • Fresh or frozen: You can use fresh or frozen vegetables — both will work great — but either way they do have to be cooked before adding to the egg mixture.
  • Cooking method: I prefer to use roasted vegetables because it imparts so much flavor, but any cooking method (steaming, boiling, or sauteing in a skillet) will also work. Be sure to pat dry if steaming or boiling.
  • Pre-cook: Pre-cooking the veggies is important to ensure that your breakfast egg muffins don’t end up soggy and watery.
• Aromatics – Not required, but I love adding some minced garlic. Caramelized onions would also be a delicious addition. For convenience, you could just whisk in 1/2 to 1 teaspoon of garlic powder or onion powder directly into the egg mixture.
• Olive Oil – For roasting the vegetables. Avocado oil works great, too.
• Meat – I didn’t add any to the basic egg muffin recipe below, but you can also add some cooked crumbled sausage, ham, or bacon. Be sure any meat you add is already cooked, because it will not cook through if you add it raw.
• Eggs – I prefer to use whole eggs, but egg whites would also work if you want egg white muffins. To do this, replace each large egg with 3-4 tablespoons of egg whites (about 1.5 egg whites).
• Milk Or Cream – Helps the eggs get fluffy! This egg muffin cups recipe is written using heavy cream, but you can swap it for the milk of your choice. Regular dairy milk or half & half will work but will increase carb count. You can also use coconut milk or almond milk for dairy-free options.
• Cheese – I used shredded cheddar, but you can also try mozzarella, gruyere, feta, or any other cheese you like. Get the full cheese list here for ideas. For a dairy-free option, simply omit the cheese (and use almond or coconut milk above).
• Sea Salt & Black Pepper

How To Make Egg Muffin Cups

This section shows how to make egg muffins in the oven, with step-by-step photos and details about the technique, to help you visualize it. For full instructions, including amounts and temperatures, see the recipe card below.

1. Cook add-ins. Toss the broccoli, cauliflower, red pepper, and garlic (or any other vegetables you are using) with the olive oil. Spread out in a single layer on a baking sheet and roast until edges are browned. If you are making your egg muffins with bacon, sausage, or other meats, pre-cook these as well.
2. Portion. Line a muffin pan with parchment paper liners or silicone cups. (You can also just spray with cooking spray, but liners make the muffins easier to remove and more portable, and require less cleanup.) Divide roasted vegetables among the cups.

3. Whisk egg base. Whisk together the eggs, heavy cream (or milk of choice), sea salt, and black pepper. Stir in cheese of your choice. Pour the mixture into the egg muffin cups.
4. Bake. They are ready when the eggs are set. Enjoy this easy breakfast recipe right away, or see storage instructions below to store for later.

How Long To Cook Egg Muffins?

With already pre-cooked meats or vegetables, bake egg muffins for 15-20 minutes.

FYI: It’s common for egg muffin recipes like this one to deflate a bit.

When they are baked, the air bubbles in the egg expand, and they deflate as they cool. One way to reduce this effect is to let the muffins cool more slowly, so keep them in the pan to cool before removing them. This will help, but know that it’s totally normal for egg muffins to collapse a little.

15 Flavor Variations

One of the best things about this egg muffin cups recipe is that it’s so versatile and easy to customize to your taste. Try these combinations for add-ins:

1. Ham & Cheese – Diced ham and chopped American (or cheddar) cheese.
2. Bacon Cheddar – Classic cooked bacon and shredded cheddar (but really, almost any cheese goes with bacon!).
3. Mushroom Swiss – Sauteed mushrooms and shredded Swiss cheese.
4. Asparagus Gruyere – Chopped cooked asparagus (a great way to use up leftover roasted asparagus!) and shredded Gruyere cheese.
5. Spinach Feta – Spinach and crumbled feta cheese. Spinach is very watery, so for spinach egg muffins, use either fresh sauteed spinach or frozen spinach drained well.
6. Garden Veggie – Bell peppers, mushrooms, onions, and chopped tomatoes (pat very dry and omit seedy parts). Cook the mushrooms and peppers, but not the tomatoes.
7. Greek – Cooked bell peppers and red onions, sliced olives, fresh basil, and crumbled feta cheese.
8. Pizza – Chopped pepperoni and shredded mozzarella. Dip in marinara sauce for serving.
9. Tex-Mex – Cooked chorizo, sauteed or roasted bell peppers, and choose from pepper jack, Cotija, or Mexican blend cheese.
10. Jalapeno Popper – Cooked bacon, chopped jalapeno peppers, sliced green onions, shredded cheddar, and small pieces of cream cheese. You only have to pre-cook the bacon (try oven bacon or air fryer bacon as hands-off methods) for this one.
11. Meat Lover’s – Sausage, pepperoni, Canadian bacon, and either cheddar or mozzarella (or both!). You can also keep it simple with sausage egg muffins only.
12. Sun-Dried Tomato & Zucchini – Sauteed zucchini, sun-dried tomatoes, and goat cheese. You’ll need to cook down the zucchini a lot, otherwise it has a tendency to get watery.
13. Garlic Parmesan – Sauteed minced garlic, Italian seasoning (or fresh herbs like pasley and chives), and shredded parmesan cheese. This version is missing bulky add-ins, so add 3-4 more eggs and an extra tablespoon or two of milk/cream to make up for it.
14. Dairy Free – Omit the cheese (replace with 1/2 cup of other add-ins) and use full-fat coconut milk (or almond milk, but coconut milk makes for a richer result) instead of heavy cream.
15. No Carb Egg Muffins – To keep carbs super low (less than 0.5g per serving), don’t include any veggies. Any combination of eggs, cream, meat, and cheeses is fine. (You can even include them on an egg fast if you make them with just eggs and cheese.)

RULE OF THUMB: The basic ratio for 12 egg muffins is 8 eggs, 1/4 cup milk of choice, 3/4 cup cheese, and 2-2.5 cups of add-ins.

The volume for the add-ins is after cooking, so you’ll start with more (about 3 cups of most vegetables will make 2-2.5 cups cooked).

Storage Instructions

• Store: Keep egg muffin cups in an airtight container in the refrigerator for up to 5 days.
• Meal prep: These are awesome for meal prep, so you can definitely make a batch ahead for quick breakfasts or snacks! Alternatively, you can cook the add-ins (vegetables and/or meats) ahead of time and bake them fresh.
• Reheat: Warm up your breakfast egg muffins in the microwave for about 30 seconds, or in the oven at 350 degrees F, until warm. Be careful not to overcook, or they will be rubbery.

Can You Freeze Egg Muffins?

Yes, you can freeze egg muffins. Let them cool completely at room temperature, then freeze in a freezer bag for 2-3 months. Thaw them in the fridge overnight before reheating.

More Healthy Low Carb Egg Recipes

If you like this breakfast egg muffin recipe, you might also like some of these other egg recipes:

bEasy Peel Hard Boiled Eggs

Egg Bites Recipe

Bacon Deviled Eggs

Egg Salad

Vegetable Frittata

Low Carb Breakfast Casserole

4.98 from 39 votes

Egg Muffin Cups

Choose from 15 flavors of this breakfast egg muffin cups recipe with veggies, eggs and cheese! It's healthy, low carb, and easy to meal prep.

Prep: 10 minutes

Cook: 35 minutes

Total: 45 minutes

Author: Maya Krampf from WholesomeYum.com

Servings: 12 (adjust to scale recipe)

Convert:

Un-save Recipe Save Recipe Go Ad-Free

Recipe Video

Tap on the image below to watch the video.

Like this video? Subscribe to my YouTube cooking channel for healthy recipes weekly! (Click the bell icon to be notified when I post a new video.)

Review Print

Pin

Ingredients

Tap underlined ingredients to see where to get them. Please turn Safari reader mode OFF to view ingredients.

• 1 cup Broccoli (cut into 1/2-inch florets) ▢
• 1 cup Cauliflower (cut into 1/2-inch florets) ▢
• 1 cup Red bell pepper (chopped into 1/2-inch pieces) ▢
• 2 cloves Garlic ▢
• 2 tbsp Olive oil ▢
• 8 large Eggs ▢
• 1/4 cup Heavy cream (or any milk of choice) ▢
• 1 tsp Sea salt ▢
• 1/2 tsp Black pepper ▢
• 3/4 cup Cheddar cheese (shredded; replace with more veggies for dairy-free) ▢

Instructions

Tap on the times in the instructions below to start a kitchen timer while you cook.

1. Preheat the oven to 400 degrees F (204 degrees C). Line a baking sheet with parchment paper or foil (grease if using foil).

2. In a large bowl, toss together the broccoli, cauliflower, red pepper, minced garlic, and olive oil.

3. Arrange the vegetables in a single layer on the baking sheet. Roast in the preheated oven for 15-20 minutes, until the edges of the broccoli are browned.

4. Meanwhile, line a muffin tin with 12 parchment muffin liners or silicone muffin liners.

5. When the vegetables are done, keep the oven on. Arrange the veggies evenly in the muffin cups.

6. Whisk together the eggs, heavy cream, sea salt, and black pepper. Stir in the cheddar cheese. Pour the egg mixture into the muffin cups over the vegetables.

7. Bake for 15-20 minutes, until the eggs are set.

Last Step: Leave A Rating!

Rate this recipe

Share your recipe picture by tagging @wholesomeyum and hashtag it #wholesomeyum on Instagram – I’d love to see it!

Readers Who Liked This Easy Recipe Also Made:

• 
  Low Carb Keto Blueberry Muffins With Almond Flour
• 
  Baked Avocado Egg Recipe (Egg Stuffed Avocado)
• 
  Coddled Eggs
• 
  Keto Pancakes (Low Carb Pancakes)

Recipe Notes

Serving size: 1 egg muffin

For other flavor options, see the blog post above.

Nutrition Facts

Amount per serving. Serving size in recipe notes above.

Calories 124

Fat 9.7g

Protein 6.7g

Total Carbs 2.5g

Net Carbs 1.8g

Fiber 0.7g

Sugar 1.2g

Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.

Course: Breakfast

Cuisine: American

Keywords: breakfast egg muffins, egg muffin cups, egg muffin recipe, keto egg muffins

Calories: 124 kcal

Want to save this recipe?

Create a free account to save your favorite recipes!

Sign Up To Save Recipes

© Copyright Maya Krampf for Wholesome Yum. Please DO NOT SCREENSHOT OR COPY/PASTE recipes to social media or websites. We’d LOVE for you to share a link with photo instead. 🙂