Spinach Egg Muffins are the meal-prep magic that you need! This low-carb, gluten-free, and keto egg muffins cups recipe is loaded with fresh spinach, cherry tomatoes, and mozzarella cheese. They’re the perfect grab-and-go breakfast bite that are also so easy to bake in the oven ahead of time!

A pile of four egg muffins are served on a white plate.

Spinach Egg Muffins Recipe

Do you roll out of bed and hear your stomach grumbling?

I know I do, and it’s awesome when I already have a healthy breakfast (like these spinach egg muffins!) ready-to-go in the fridge.

Let’s be honest, most of us don’t want to get up even 5 minutes earlier in the morning in order to make a healthy breakfast. I’m totally with you!

So on those weekday mornings when you snooze just one time too many and find yourself rushing out the door, you’ll be thankful you prepared a batch of these low-carb, keto, and veggie-loaded egg cups ahead of time!

Plus, you can feel fancy since these spinach egg cups are basically mini frittatas.

Be sure to check out these other delicious variations of Breakfast Egg Muffins.

Eggs, milk, spinach, tomatoes, and seasonings are the basic ingredients for this recipe.

Ingredients

The delicious ingredients you’ll need for these healthy egg muffin cups are super simple to find:

  • Eggs. You’ll need 10 large eggs. Organic and either pasture-raised or free-range eggs taste the best. They’re also the healthiest option for you.
  • Milk. Some type of milk will be mixed together to help fluff up the eggs. Cashew milk was tested in this recipe, but soy, almond, oat, 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. This isn’t necessary but it does add a nice little bite to counteract the savory fillings. You can also toss in some finely chopped sweet or green onions if you’d prefer.
  • Cheese. Shredded mozzarella cheese is the pick of chose. It pairs wonderfully with the spinach and tomatoes. It’s not necessary to add cheese, so you can leave it out if you’re on a dairy-free diet. If needed, you can sub in another type of cheese, cheddar cheese or Parmesan cheese if you would like, though.
  • Spinach. Fresh spinach leaves are thinly sliced and then mixed into the scrambled eggs. There’s no need to sauté them ahead of time – they’ll cook up full when the muffin cups are baking in the oven. You can use fresh baby spinach or regular leaves.
  • Tomatoes. Cherry or grape tomatoes are preferred since they have less juice and pack more flavor. Vine-ripened or Roma tomatoes may be used, but just make sure you completely seed them before dicing.

How to Make Egg Muffins

The basic steps for making this egg muffin recipe are super simple to follow:

Best Muffin Tin

One of the biggest frustrations with making egg muffins at home is that they end up sticking to the muffin pan.

If this happens to you, chances are it’s the type of muffin tin that you’re using.

In order to avoid this sticky situation, 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.

Make the Egg Mixture

You need to preheat the oven to 350°F early so it has time to warm up completely.

Combine the whole eggs, milk, salt, pepper, garlic powder, and onion powder in a large mixing bowl, one that is big enough to whip up the mixture.

Thoroughly whisk the ingredients until they’re fully incorporated.

Prep the Muffin Tins

This recipe cooks best in a 12-count muffin pan. Spray it thoroughly with a non-stick cooking spray. Be liberal so the eggs don’t stick to the sides.

Fill each well up halfway with the egg mixture. If you go over this the muffins will puff up too much and deflate after baking.

Add the Filling and Bake

Add filling spinach, tomatoes, and cheese into each cup. Stir ingredients with a spoon until well combined. 

Bake egg muffins in preheated 350°F oven for 22-24 minutes. You’ll know they’re done baking when they puff up and the middles no longer jiggle.

Cheese is sprinkled by a hand into the egg muffin mixture.

Meal Prep & Storage

  • To Prep Ahead: Egg muffins make a wonderful grab-and-go breakfast for busy morning. Simply prep the entire tray of muffins ahead of time and pull them out when you need them throughout the week!
  • To Store: 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 freezer bag and store for up to 2-3 months.
  • To Reheat: Add egg muffins to microwave and cook for 30-45 seconds.

What is the best muffin tin for egg muffin cups?

For the best results, use a clean, non-stick muffin tin that is in good condition. If the non-stick coating is flaking off, the eggs will stick to the side. Also, don’t use muffin liners on these healthy breakfast egg muffins.

Can I make egg white muffins?

You can definitely make Egg White Muffins, they are both flavorful and healthy. Simply remove the yolks before mixing in the other ingredients. You get all the protein of the eggs but less calories without the yolks. Egg whites are a great way to have a low carb, low calorie, and high-protein breakfast.

Can you freeze egg muffins?

Egg muffins are one of the best breakfast recipes to freeze. They are easy to whip up, freeze well, and are perfect to have on hand for busy mornings. These make the perfect quick breakfast to start your day.

Are egg muffins healthy?

When you make egg muffins with healthy fillings, like spinach and tomatoes, they are a good-for-you breakfast that can start your day right.

How long do egg muffins last in the fridge?

After you bake the egg muffins, they will last in the fridge for up to 3 to 4 days. Be sure to store them in an airtight container so they stay as fresh as possible. Make up a big batch at the beginning of the week so you have breakfast ready when you need it.

An overhead shot of spinach egg muffins with tomatoes are served for a low-carb breakfast.

Dietary Modifications

The recipe you’ll find below is already gluten-free, low-carb, keto and vegetarian as written. Here are some adjustments you can make to help it fit your other dietary requirements:

  • Paleo & Whole30: Leave out the cheese to make it Paleo and Whole30.
  • 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.

Expert Tips and Tricks

  • Use a non-stick pan. The eggs will stick if your muffin cup tray has been scratched up from too many uses.
  • Spray it down. A big issue with removing your healthy egg muffins is their tendency to adhere to the pan. So use a newer tray and use a good amount of nonstick spray!
  • Meet halfway. The spinach egg muffins will puff up while baking, so make sure you do not fill them too full!
  • Give it a chop. Dicing all of the filling ingredients will ensure you have a bit of all of them in every bite.
  • Change it up. You can easily adapt this recipe to include your favorite fillings. Or, add in some spices, like Italian seasoning, for a real treat.
Fresh spinach and tomatoes are served around a pile of spinach egg muffins.

More Egg Recipes

Eggs are the best way to start your morning, or enjoy a snack later in the day. Check out these healthy breakfast recipes and afternoon snacks next.

Sweet Potato Hash with Eggs and Breakfast Potato Hash with Bacon and Eggs are both healthy and delicious.

For a lighter start, go with this Easy Crustless Spinach Quiche or Baked Frittata with Pesto.

Classic Deviled Eggs are a crowd pleaser. Try making them with Instant Pot Hard Boiled Eggs or Air Fryer Hard Boiled Eggs.

Tap stars to rate!

4.55 from 22 votes

Spinach Egg Muffins Recipe

Healthy Spinach Egg Muffins with Tomatoes are a great make-ahead low-carb, gluten-free, and keto breakfast recipe for those hectic weekday mornings.  Low-carb egg muffin cups are loaded with spinach, fresh mozzarella, and roma tomatoes for the perfect grab-and-go breakfast!
Tomato, spinach, and cheese egg muffins are stacked on a plate for breakfast.
Yield 12 muffins
Prep 5 minutes
Cook 25 minutes
Total 30 minutes
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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
  • ¾ cup spinach thinly sliced
  • ¾ cup grape tomatoes quartered
  • ¾ cup Mozzarella cheese shredded

Instructions 

  • Preheat oven to 350 degrees.
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.
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.
Last step! If you make this, please leave a review letting us know how it was!

Tap stars to rate!

4.55 from 22 votes

Video

Notes

Meal Prep & Storage

  • To Prep Ahead: Egg muffins make a wonderful grab-and-go breakfast for busy morning. Simply prep the entire tray of muffins ahead of time and pull them out when you need them throughout the week!
  • To Store: 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 freezer bag and store for up to 2-3 months.
  • To Reheat: Add egg muffins to microwave and cook for 30-45 seconds.
 
 

Nutrition

Calories: 77kcal, Carbohydrates: 1g, Protein: 6g, Fat: 5g, Saturated Fat: 2g, Trans Fat: 1g, Cholesterol: 142mg, Sodium: 264mg, Potassium: 92mg, Fiber: 1g, Sugar: 1g, Vitamin A: 499IU, Vitamin C: 2mg, Calcium: 66mg, Iron: 1mg

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

Made this recipe?Leave a comment below!
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Comments

    1. Yay! So happy to hear you enjoyed the recipe, DiAnne! They’re perfect to share. Thanks so much for taking the time to leave a comment and rating!

  1. 5 stars
    I substitute the tomatos for small chopped red pepper, used frozen spinach. I added 3 small links of Brown ‘N Serve turkey sausage finely chopped therefore l only used 1/4 teaspoon of salt.
    My husband and my family loved it.
    Thank you for the recipe.

    1. Yay! So happy to hear you enjoyed the recipe, Zully! I’m glad your family loved it. Thanks so much for taking the time to leave a comment and rating!

    1. Yay! So happy to hear you enjoyed the recipe, Elizabeth! Thanks so much for taking the time to leave a comment and rating!

    1. No, I haven’t tried making this into a casserole. But, I would suggest using an 8×10-inch and bake at 350. Then, check after 15 minutes or so. Hope this helps!

  2. 5 stars
    Hi..I am very new on your mailing list..I liked your awesome recipes and weekly meals but could not post them to my social media accounts such as:Facebook..Twitter..Yummly and or Tumblr..I could save them only on Pinterest.Please comment

    1. I am so happy you enjoy the recipes and have joined the mailing list!! If you would like to share recipes on Facebook or twitter you can copy and paste the URL into those apps. Currently, I do not have a button for you to click to share from the site, but have considered adding them! Thanks for your question!

  3. Thanks London, I really enjoy your food e-mails, as I am a celiac and am lactose intolerant also. There are great recipes I can eat. I really look forward to seeing what new recipes I can try.

    1. Thank you Susan! I am so happy I can help you out. We do a lot of gluten-free and dairy-free recipes in our house, so you’ve come to the right place 🙂 Thanks so much for your comment!