Keto Egg Muffins Recipe (Egg Muffin Cups)

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One batch of these low carb keto egg muffins and you’ll never want to live without them in your fridge again! Egg muffin cups make a great meal prep low carb breakfast (or lunch!) for busy days, whether your rushing out the door in the morning, or rushing to get to your computer like me. This easy egg muffin recipe is made with veggies, eggs, milk of choice, and cheese, but I also have 15 variations and a formula for the ratios below, so you can customize it to your heart’s content. If you prefer plain eggs, try these oven baked eggs or cloud eggs instead — or sausage egg muffins for a meatier option!

Keto breakfast muffins can mean lots of things — they can be sweet like a low carb blueberry muffin — but this time around, we’re making them with eggs. These are naturally low carb, but also make a convenient meal prep breakfast for the whole family. Pair them with some keto coffee for a healthy, filling breakfast.

These quickly became part of my breakfast rotation of keto oatmeal, chaffles, and of course, fathead cinnamon rolls for holidays and weekends! You can even include these muffins on an egg fast if you make them with just the egg and cheese, and skip the veggies.

What Are Egg Muffins?

Egg muffins (often referred to as egg muffin cups or omelet muffins) are single-serve mini frittatas made in a muffin tin. This is why they are also sometimes called egg frittata muffins. They typically contain eggs, milk, cheese, and veggies, meats, or both.

Ingredients For Keto Egg Muffins

This section explains how to choose the best ingredients for healthy egg muffins, 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.
  • Watch the carbs: If you want keto egg muffins, avoid high-carb add-ins like potatoes (including white or sweet potato). Most veggies will be low carb, but check the keto vegetables to be sure.
• Aromatics – Not required, but I love adding some 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 or bacon. Be sure any meat you add is already cooked, because it will not cook through while baking egg muffins.
• 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 – This recipe is written using heavy cream, but you can swap it for the milk of your choice. Regular dairy milk will work but will increase carb count. You can also use coconut milk, coconut cream, or almond milk.
• 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.
• Sea Salt & Black Pepper

You probably have most of the ingredients you need to make these yummy baked egg muffin cups already!

How To Make Egg Muffins In The Oven

This section shows how to make egg muffins, with step-by-step photos and details about the technique. For full instructions, see the recipe card below.

• 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.
• Portion. Line a muffin tin with liners or silicone cups and divide roasted vegetables between the 12 wells.

• Whisk. Mix 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.
• Bake. They are ready when the eggs are set.

How Long To Cook Egg Muffins?

Bake egg muffins for 15-20 minutes, in addition to the 15-20 for the roasted vegetables. The good news is most of the time is hands-off, so the active prep is only around 10 minutes.

15 Flavor Variations

There are almost endless variations for these! One of the best things about this breakfast egg muffin cups recipe is that it’s so versatile and easy to customize. 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 cooked fresh 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 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!).
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.

RULE OF THUMB: The basic ratio for 12 egg muffin cups 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).

Frequently Asked Questions

Should I use a large or small muffin tin?

It’s up to you! This recipe is written using a large muffin pan (I love this one!), but you can easily use a small muffin tin — you’ll get about twice as many muffins.

Why do my egg muffins collapse?

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 and fine for egg muffins to collapse a bit.

How many carbs in keto egg muffins?

The carbs in healthy breakfast egg muffins will depend on what add-ins you put in. For the recipe below with broccoli, cauliflower, bell peppers, and cheddar, each egg muffin has 1.8 grams net carbs.

How many keto egg muffins can I eat?

Egg muffins will vary in serving size. I have one serving listed as one egg muffin, but nutrition needs will really vary person to person. You might eat 2 or 3 for a meal.

Use this macro calculator to help you figure out what your macros should be, depending on your goals. This will give you an outline for what your meals should look like.

Storage Instructions

Breakfast egg muffins are awesome for meal prep, so you can definitely make a batch ahead for quick breakfasts or snacks. Store them in the refrigerator for 4-5 days.

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.

Reheating instructions:

Reheat your keto breakfast 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.

More Healthy Low Carb Egg Recipes

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

• Easy Peel Hard Boiled Eggs
• Instant Pot Egg Bites
• Deviled Eggs
• Egg Salad
• Veggie Omelette

4.97 from 32 votes

Keto Egg Muffins Recipe

Learn how to make egg muffins for a grab-and-go breakfast you can meal prep, with 15 flavor variations! You'll love this healthy keto breakfast egg muffin cups recipe.

Prep: 10 minutes

Cook: 35 minutes

Total: 45 minutes

Author: Maya Krampf from WholesomeYum.com

Servings: 12 (adjust to scale recipe)

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Ingredients

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• 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.

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Recipe Notes

Serving size: 1 egg muffin

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

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