Super fluffy and loaded with your favorite fillings, these Breakfast Egg Muffins are so easy to make and super healthy for you! Scrambled eggs are whisked together, poured into a muffin tin, and then baked in the oven to make the cutest mini egg frittatas. This low-carb and keto egg cup recipe is a great base for a ton of filling options: bacon and cheddar, ham and Swiss cheese, or a veggie version with tomatoes and spinach!
Breakfast Egg Muffins Recipe
On-the-go or chilling at home, these egg muffins are one of the fastest and easiest breakfast recipes you can make!
They’re great for prepping ahead of time and reheating throughout the week.
You can double the recipe and feed a small crowd for Easter or Mother’s Day brunch.
Or just make them on a whim when you’re craving a fancy frittata in a cuter miniature version. (Yes, these egg muffin cups are essentially like a mini frittata!)
With the basic recipe you’ll find below you can then get creative with whatever fillings you choose!
From more meat-heavy fillings like bacon and ham to a strictly vegetarian spinach egg muffin – there’s something here that everyone will love!
Savory Ingredients
The basic ingredients you’ll need for these egg muffins are super simple to find:
- Eggs – You’ll need 10 large eggs. Organic and pasture-raised eggs taste the best and are the healthiest option for you, but you can use whatever eggs you have on hand.
- Milk – Some type of milk will be mixed together to help fluff up the eggs. Cashew milk and almond milk have been tested in this recipe, but soy milk or regular milk may also be used.
- Garlic Powder – An absolute must! If you want, you can also whisk in two cloves of crushed garlic instead.
- Onion Powder – Not necessary, but this adds a nice little bite to counteract the savory fillings. You can also toss in some finely chopped onions if you’d prefer.
- Cheese – Some type of shredded cheese, such as cheddar, Mozzarella, or swiss was used in all of these muffins. It’s not necessary to add cheese, so you can leave it out if you’re on a dairy-free diet.
- Meat – Cubed ham and crumbled bacon were mixed into two of the versions you’ll find below. You can also leave these out if you’re vegetarian and replace with additional vegetables.
- Vegetables – Tons of vegetables would taste great inside these egg frittata muffins. Chopped cherry tomatoes and thinly sliced spinach were used in the muffins you see here, but you can also try bell peppers, onions, kale, and mushrooms.*
- Herbs – Finely chopped fresh herbs brighten up the look and flavor of these egg muffins. Parsley and chives are great additions but thyme, rosemary, and oregano may also be used. Dried herbs can be replaced with fresh. Just make sure you reduce the amount used to 1/3.
*Pro Tip: If using heartier vegetables, like potatoes, beets, or carrots, make sure you cook them partially before mixing in.
Best Muffin Tin
One of the biggest obstacles most home-cooks run into when making breakfast egg muffins is that they end up sticking to the muffin tin.
This happened to me on numerous occasions. And the main culprit? The muffin pan I was using was old and no longer non-stick.
In order to avoid this sticky egg mess, there are 2 types of muffin tins you can use:
- Non-stick muffin pan. The key here is to make sure it is still non-stick. If you see any scratches on your pan, or if you’ve had it for years and have made dozens of muffins in it, then it’s probably not as non-stick as you’d like. If this is the case, you can always buy a new non-stick muffin pan.
- Ceramic-coated muffin pan. This is probably the best option since it is the most non-stick of the pans. If you don’t already have one, this ceramic muffin pan is great.
*Pro Tip: If you’re still nervous about your egg muffin cups sticking to the pan you can always use a parchment paper muffin cup liner. Do NOT use a regular paper liner as the eggs will stick mercilessly to it.
How to Make Egg Muffins
The basic steps for making egg muffins are super simple to follow:
- Preheat oven to 350°F.
- In a large bowl combine eggs, milk, salt, pepper, garlic powder, and onion powder. Whisk until well combined.
- Spray a 12-count regular-sized muffin cup tray with non-stick cooking spray. Make sure you completely coat the cavities so the eggs don’t stick!
- Fill each muffin cup to ½ full with the egg mixture. If you go over this the muffins will puff up too much and deflate after baking.
- Add filling ingredients into each cup and stir with a spoon until well combined. Read below about more filling option ideas.
- Bake egg muffins in preheated 350°F oven for 22-24 minutes.
3 Filling Options
One of the best things about making breakfast egg muffins is how versatile they can be! You can add in almost any filling ingredients you’d like. Here are some of the most popular filling options to try out:
- Bacon + Cheddar + Parsley
- Cubed Ham + Swiss Cheese + Chives
- Cherry Tomatoes + Spinach + Mozzarella
Other Filling Ideas
While the three filling options above are my go-tos, there are also numerous other fun ingredients you can throw in. Here are some other filling ideas for baked egg muffins:
- Ground Sausage, Chicken, Beef
- Artichokes, Eggplant, Bell Peppers, Broccoli
- Carrots, Potatoes, Sweet Potatoes (make sure to cook these before adding in.)
- Basil, Dill, Cilantro, Rosemary, Thyme
Meal Prep and Storage
To Prep Ahead: Egg muffins make a wonderful grab-and-go breakfast for busy weekdays. Simply prep the entire tray of muffins ahead of time and pull them out when you need them throughout the week!
To Store:Â Store egg muffins in an airtight container in the refrigerator for up to 3-4 days.
To Freeze: Wrap egg muffins individually in wax or parchment paper. Place in a freezer safe container or ziploc bag and freeze for up to 2-3 months.
To Reheat: Add egg muffins to microwave and cook for 30-45 seconds.
Dietary Modifications
The recipe you’ll find below is already gluten-free and low-carb as written. Here are some adjustments you can make to help it fit your other dietary requirements:
Vegetarian: Opt for a veggie-only filling. Leave out the meat products.
Keto: Stick to lower-carb veggies, meat, and cheese fillings. Leave out the tomatoes, potatoes, or other starchy-vegetables.
Paleo: Leave out the cheese to make it Paleo.
Whole30: Leave out the cheese and use sugar-free bacon.
Dairy-Free: Leave out the cheese or replace it with a dairy-free cheese alternative.
Nut-Free: Use regular milk or soy milk instead of a nut-based milk.
FAQs
Why are my egg muffins spongy?
Over-beating the eggs while scrambling can lead to dense and spongy egg muffins. Beat the eggs until just combined for the best texture.
How do you keep egg muffins from deflating?
Inevitably, egg muffins will deflate some after baking. However, if you allow them to cool down inside the muffin tin this will prevent some of the drastic deflating that could happen.
How long do egg cups last?
Baked egg cups will last in the refrigerator for up to 3-4 days and in the freezer for up to 2-3 months.
What can I make with too many eggs?
If you have too many eggs you can make hard-boiled eggs, avocado egg salad, deviled eggs, or breakfast egg muffins.
Pro Tips and Tricks
- Use a non-stick muffin tin. Eggs have a tendency to stick to older and not-so-non-stick baking pans.
- Non-stick cooking spray is a must. If you’re worried about your eggs sticking, this will do the trick!
- Allow egg muffins to cool in the muffin tin. This will prevent them from deflating too much.
- Finely chop all of the filling ingredients.  Doing this will ensure you have a bit of all of them in every bite.
- Use whatever leftovers you have in the fridge! Chop up any extra veggies, meats, or herbs and throw them into your egg muffins for the week!
Breakfast Egg Muffins Recipe
Super fluffy and loaded with your favorite fillings, these Breakfast Egg Muffins are so easy to make and super healthy for you! Scrambled eggs are whisked together, poured into a muffin tin, and then baked in the oven to make the cutest mini egg frittatas. This low-carb and keto egg cup recipe is a great base for a ton of filling options: bacon and cheddar, ham and Swiss cheese, or a veggie version with tomatoes and spinach!
Ingredients
- 10 eggs
- ¼ cup milk cashew, almond, or regular milk
- 1 tsp. salt
- ¼ tsp. black pepper
- ¼ tsp. garlic powder
- ¼ tsp. onion powder
Bacon Egg Muffins
- 5 strips bacon cooked and crumbled
- ¾ cup cheddar cheese shredded
- ¼ cup parsley finely chopped
Ham Egg Muffins
- ¾ cup ham cubed
- ¾ cup Swiss cheese shredded
- ¼ cup chives finely chopped
Spinach Egg Muffins
- ¾ cup spinach thinly sliced
- ¾ cup grape tomatoes quartered
- ¾ cup Mozzarella cheese shredded
Instructions
-
Preheat oven to 350°F.
 In a large bowl combine eggs, milk, salt, pepper, garlic powder, and onion powder. Whisk until well combined.
-
In a large bowl combine eggs, milk, salt, pepper, garlic powder, and onion powder. Whisk until well combined.
-
Spray a 12-count regular-sized muffin cup tray with non-stick cooking spray. Make sure you completely coat the cavities so the eggs don’t stick!
-
Fill each muffin cup to ½ full with the egg mixture.

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Bacon Egg Muffins: Fill each cup with 1 tablespoon crumbled bacon, 1 tablespoon shredded cheese, and 1 teaspoon chopped chives.
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Ham Egg Muffins: Fill each cup with 1 tablespoon cubed ham, 1 tablespoon shredded cheese, and 1 teaspoon chopped chives.
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Spinach Egg Muffins: Fill each cup with 1 tablespoon spinach, 1 tablespoon tomatoes, and 1 tablespoon shredded cheese.
-
Stir the fillings into the scrambled eggs with a spoon until all ingredients are well combined. 
Bake egg muffins in preheated oven for 22-24 minutes.
-
Serve immediately or refrigerate and enjoy for up to 3-4 days.
Recipe Video
Recipe Notes
- The measurements for the bacon, ham, and spinach egg muffin ingredients are for a batch of 12. If you would like to make 4 of each simply divide the ingredient amounts by 3.
Pro Tips and Tricks
- Use a non-stick muffin tin. Eggs have a tendency to stick to older and not-so-non-stick baking pans.
- Non-stick cooking spray is a must. If you're worried about your eggs sticking, this will do the trick!
- Allow egg muffins to cool in the muffin tin. This will prevent them from deflating too much.
- Finely chop all of the filling ingredients.  Doing this will ensure you have a bit of all of them in every bite.
- Use whatever leftovers you have in the fridge! Chop up any extra veggies, meats, or herbs and throw them into your egg muffins for the week!
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