Low Carb Keto Egg Muffins (Egg Muffin Cups Recipe)

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One batch of these 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 egg muffin recipe features something special… roasted vegetables! It gives the breakfast egg muffins incredible flavor AND makes veggies for breakfast totally delicious. Pair the low carb egg muffins with some butter coffee or my 90-second keto bread for a healthy, filling breakfast.

Keto breakfast muffins can mean lots of things – they can be sweet like a 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, even if they aren’t.

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. Let me know what you think about them.

This keto egg muffins recipe was originally published on August 26, 2017, and the post was republished in December 2020 to add updated pictures, useful tips, and some improvements to keto breakfast egg muffins. The original version did not include cheese, but I added it in because… cheese!! You can easily skip it if you like, though.

Keto Egg Muffins Ingredients

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

• Low carb vegetables of your choice – I used broccoli, cauliflower, and red bell pepper
• Garlic
• Olive oil
• Eggs
• Heavy cream
• Salt & pepper
• Cheese of your choice – I used cheddar

(See below for variation ideas and swaps!)

How To Make Breakfast Egg Muffins

These easy low carb egg muffins are quick to make:

• Roast. Toss broccoli, cauliflower, red pepper and garlic with the olive oil. Spread out in a single layer on a baking sheet and roast until edges are browned.

TIP: While you may be tempted to skip roasting the vegetables, I urge you do it! The roasted veggies are the best part of these healthy egg muffins. Roasting them imparts so much more flavor than the usual steaming method, plus it ensures that your breakfast egg muffins don’t end up soggy and watery. This is why cooking the veggies is required.

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

• Whisk. Whisk the eggs, heavy cream, sea salt, and black pepper together until combined. Stir in shredded cheddar and pour into the egg muffin cups.

• Bake. They are ready when the eggs are set

How long to cook egg muffins?

For this recipe, the 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.

Variations For Egg Muffins

How to customize them:

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

Here are some of the components you can change up:

• Vegetables – Make it your own depending on what keto veggies you love, or what you have in your fridge right now! I do recommend avoiding watery vegetables, like zucchini, which would make the egg muffins watery, too. (If you want to use your zucchini, try zucchini pizza bites or zoodles instead.)
• Cheese – I used cheddar, but you can also try mozzarella, gruyere, feta, or any other cheese you like. Get the full cheese list here for ideas.
• 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.
• Meat – I didn’t add any, but you could also add some cooked crumbled sausage or bacon.

How to make keto egg muffins dairy free:

Yes, this recipe can easily be made dairy-free, paleo, and whole30. Simply omit the cheese (replace with the same amount of additional veggies) and use coconut cream instead of heavy cream.

Can I use frozen vegetables?

Yes! I used fresh veggies, but you can roast frozen ones, too. Just make sure they aren’t watery when they are done, before adding them to the cups.

Should I use a large or small muffin tin?

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

Egg Muffin Cups FAQs

How many carbs in keto egg muffins?

The carbs in healthy breakfast egg muffins will depend on what other ingredients are included in them.

In this recipe, 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.

Check out my 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.

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 found in egg expand. One they start cooling? They deflate.

One way to help prevent or at least help this from happening is to let the muffins cool slower, so keep them in the pan until cool before removing them. This will help a bit, but know that it’s totally normal and fine for egg muffins to collapse a bit.

Egg Muffin Recipe Storage Instructions

Can you make these ahead?

Yes, take these low carb breakfast egg muffins to go! They can be made ahead for quick breakfasts and/or snacks.

How to store keto egg muffin cups:

Store the egg muffins in the refrigerator for 3-5 days.

Can you freeze keto egg muffins?

You can freeze the egg muffins. Freeze in a single layer until frozen solid, then transfer them to a freezer bag for 2-3 months. Thaw them in the fridge overnight before reheating.

How to reheat breakfast egg muffin cups:

Reheat these muffins in the microwave for about 30 seconds, or until heated through. You can also reheat in a 350 degree F oven.

More Keto Egg Recipes

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

• Easy Peel Hard Boiled Eggs – The ultimate guide to perfect hard boiled eggs every time! Plus a time chart so you can cook them exactly the way you like them.
• Instant Pot Egg Bites – This recipe from This Old Gal features red peppers and feta for a twist on egg bites.
• Deviled Eggs – What makes the best deviled eggs even better? BACON! Made with basic ingredients and ready in 20.
• Keto Egg Salad – Just 5 minutes to make this classic. Use it on salads, for low carb sandwiches, and lettuce wraps.
• Veggie Omelette – Another way to enjoy eggs and veggies together, including the trick to a light and fluffy omelette.

• 3-Compartment Glass Meal Prep Containers – Pop a few low carb egg muffins in here with a side of green salad and macadamia nuts and you’ve got a nutritious breakfast that’s quicker than the drive-thru.
• Muffin Tin – This one is my favorite.
• Muffin Liners – A must for easy cleanup! You can use silicone muffin liners or parchment liners. Both can be used for keto chocolate cupcakes as well.

Low Carb Egg Muffins Recipe:
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Low Carb Keto Egg Muffins (Egg Muffin Cups Recipe)

See how to make easy keto egg muffins for a grab-and-go breakfast you can meal prep! This method (with variations!) makes the best breakfast egg muffin cups recipe.

Course Breakfast

Cuisine American

Keyword breakfast egg muffins, egg muffin cups, egg muffin recipe, keto egg muffins, low carb egg muffins

Calories 124 kcal

Prep Time 10 minutes

Cook Time 35 minutes

Total Time 45 minutes

Author Maya Krampf from WholesomeYum.com

Servings 12 muffins

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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 coconut cream for dairy-free)
• 1 tsp Sea salt
• 1/2 tsp Black pepper
• 3/4 cup Cheddar cheese (shredded; replace with more veggies for dairy-free)

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Instructions

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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 muffin

Video Showing How To Make Egg Muffin Cups:

Scroll up a bit to see the video for this recipe -- it's located directly above the ingredients list. It's the easiest way to learn how to make Egg Muffin Cups!

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.

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