Whole30 Cheesy Broccoli Egg Muffins

Cheesy broccoli egg muffins are the perfect breakfast and can easily be made ahead of time, great for busy mornings!

These dairy free cheesy broccoli egg cups are made with just 6 ingredients and are delicious hot, cold or room temperature! Packed with veggies, these egg muffins are dairy free, gluten free, low carb, Whole30, vegetarian and paleo friendly.

Two cheesy broccoli egg muffins stacked on a plate.
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Why you will love this recipe

  • If you have trouble getting in veggies in your morning routine, you have to try these delicious cheesy broccoli egg muffins! The broccoli is finely chopped and blends nicely in the back to the sundried tomato and cheesy flavors of the muffin.
  • Great for meal prep or batch cooking! If you ever struggle with not having enough time to cook a fresh breakfast, these broccoli cheese egg muffins are the perfect solution! Just bake up a big batch on the weekend and you can eat them cold in the car or warm them up in the microwave on your way out the door!
  • These broccoli egg muffins are so easy to make! The broccoli gets chopped down using a food processor, but if you are short on time, you could also use cauliflower rice or broccoli rice bought at the store pre-chopped.
  • These Whole30 broccoli cheese muffins are made with nutritional yeast  instead of cheese, making them dairy free with all the cheesy flavor! You will not believe how delicious these are without the cheese!


  • Broccoli
  • Eggs
  • Egg Whites
  • Salt
  • Garlic Powder
  • Nutritional Yeast
  • Sundried Tomatoes

How to make cheesy broccoli egg muffins

  1. Preheat the oven to 400F and chop the broccoli into 1-2 inch pieces (florets and stalk) and process the broccoli in the food processor until it resembles large pieces of rice. If you do not have a food processor, just chop the broccoli by hand into very small bits.
  2. Preheat a large skillet over medium heat. Add nonstick spray and add broccoli to cook 3-5 minutes, stirring occasionally. Alternatively, you can cook the broccoli in the microwave (2-3 minutes) or leave it raw.
  3. In a small mixing bowl, combine the eggs and egg whites, taking the time to really beat them together to break up the egg whites.
  4. In a mixing bowl, combine the cooked broccoli, salt, garlic powder, nutritional yeast and sundried tomatoes. Stir well to fully coat the broccoli.
  5. Add the eggs to the broccoli mixture and stir well.
  6. Add silicone liners, parchment paper liners to a muffin tin or use a silicone muffin tray (my preferred method). Use a ¼ cup measuring cup to divide the broccoli egg mixture between the muffin cavities.

    Steps on how to make cheesy broccoli egg muffins.
  7. Bake in the oven for 20-22 minutes.
  8. Take out of the oven and allow to cool slightly before removing to fully cool on a wire rack on the counter.

    Broccoli cheese egg muffins before and after baking.

What you need to make this recipe

Other fun additions

To add more protein: You can stir in cooked bacon, turkey bacon, sausage, white beans or even hemp hearts.

To add more veggies: Bulk up the broccoli muffins even more with things like roasted red pepper, tomatoes, chopped asparagus, cooked zucchini, cooked onions, cooked mushrooms, spinach, kale, jalapenos, etc.

Whole30 cheesy broccoli egg muffins in a muffin tin.

Top tips

Eggs love to stick to traditional muffin tins. I would not recommend pouring eggs into a regular greased muffin tin. To make clean up easy, I would recommend using silicone muffin liners (they are re-usable and don’t stick to eggs). You can also try parchment paper liners (however I’ve had eggs stick to these as well.

The best thing to make egg muffins in is a silicone muffin tin. The eggs never stick, they are easy to pop out after baking and it’s so easy to clean. These are well worth the investment!

I find that veggies often release water when they are cooking so I like to quickly saute veggies to help release some of that water before adding it to the egg cups. Cooking the broccoli ahead of time is a personal preference, but if you have the time, I would highly recommend you sauté the veggies first.

What can you serve with egg muffins

These cheesy broccoli egg muffins are great on their own, especially if you are on the go for breakfast or just need something quick. However, you can always prep some other foods ahead to serve with these egg cups. Some other ideas include:

Add more protein: with turkey bacon, bacon, breakfast sausage or chicken sausage or white beans.

Add more veggies: You can prep a nice salad to go along side of these broccoli cheese cups, like this shredded brussel sprouts salad with creamy balsamic dressing, or you could serve some quick air fryer brussel sprouts on the side.

Add a sauce for dipping: These broccoli egg muffins would be great dipped or topped with some homemade pesto or homemade ketchup!

How to store broccoli egg muffins

These are even better the next day, so they are fantastic for meal prep! You can store these broccoli cheese muffins in the fridge for up to 5 days in an airtight container.

You can also freeze these broccoli muffins, however I find that if the egg cups are frozen too quickly, they can retain a lot of water and be mushy when defrosted. To preserve the texture, first let the eggs cool completely in the fridge (overnight is best). Transfer the egg muffins right to the freezer in an freezer safe container with as much of the air removed as possible, this helps reduce the amount of large ice crystals that form in the muffins (which makes them watery when defrosted). . Freeze for up to 2 months.

Defrost broccoli muffins in the fridge overnight for the best texture/taste.

Egg muffins on a white plate with a bite taken out of one.

Broccoli egg muffins common questions

Can you use frozen broccoli?

Yes! You can use frozen broccoli in this recipe. I would recommend defrosting it first, before adding it to the food processor. Frozen broccoli tends to release more water when cooking, so you may need to saute it for an extra 1-2 minutes to cook off the excess water!

Can you use all egg whites?

This recipe uses a mix of eggs and egg whites. I like to add the egg whites to add protein without all the added fat. If you want to use all egg whites in this recipe, you will likely need 12-15 eggs (1 cup-1.25 cups).

Can you use all eggs (no egg whites)?

Yes! This recipe adds the egg whites for protein, but if you like to use the whole egg, you can use 8 whole eggs instead of eggs + egg whites.


Broccoli: If you do not like broccoli or are out of it, you can also use cauliflower or any of the veggies listed above in the “other additions” section.

Nutritional yeast: Nutritional yeast is what adds the cheesy flavor to these muffins. If you don’t have nutritional yeast, you will be missing out on that cheesy flavor. If you have a dairy free cheese (or tolerate regular cheese), you could add ½ cup of cheese to the mixture for that cheesy flavor.

Sundried tomatoes: Sundried tomatoes are totally options but do add that nice umami factor to these egg cups. I highly recommend the sundried tomatoes in olive oil (I buy mine at Trader Joe’s but you can also find large jars at places like Costco, BJ’s, Sam Club). No need to find a replacement for these if you cannot find them.

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Hand holding broccoli cheese egg cups.

Whole30 Broccoli Cheese Muffins

Cheesy broccoli egg muffins are the perfect breakfast or healthy snack! Made with just 6 ingredients and packed with protein and veggies! Dairy free, gluten free, Whole30 and paleo friendly!
5 from 1 vote
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Course: Breakfast, Snack
Cuisine: American
Keyword: Broccoli Cheese Muffins, whole30 broccoli egg muffins
Prep Time: 6 minutes
Cook Time: 30 minutes
Total Time: 40 minutes
Servings: 4



  • Preheat oven 375F
  • Add the broccoli florets and broccoli stem to the food processor (break into small chunks) and pulse until it has a riced consistency.
  • Preheat a skillet over medium heat and spray with olive oil. Add riced broccoli and cook 4-5 minutes. Stir occasionally.
  • In a small bowl, combine the eggs and egg whites and whip together well to fully incorporate the whites.
  • When the broccoli is done cooking, add broccoli to a large bowl and add salt, garlic powder, nutritional yeast and sundried tomatoes to the broccoli and stir well making sure everything is well combined.
  • Pour the eggs over the broccoli mixture and stir well.
  • Add silicone liners or parchment paper liners to a muffin tin and using the 1/4 cup measuring cup, divide the egg and broccoli mixture between 12 muffin cups.
  • Bake at 375 for 26 minutes.
  • Remove from oven and allow to cool slightly. Eat hot, or allow to come to room temperature and store in the fridge for up to 4 days.


Note: 6 egg whites = 3/4 cup of egg whites.
The best thing to make egg muffins in is a silicone muffin tin. The eggs never stick, they are easy to pop out after baking and it’s so easy to clean (because nothing sticks). If you do not have a silicone muffin tin, you can also use silicone muffin liners or parchment paper muffin liners. 
Store these in the fridge for up to 5 days or in the freezer for up to 2 months. Note: before freezing allow these cheesy broccoli egg muffins to cool completely in the fridge. This will help reduce the amount of large ice crystals that form in the freezer. Be sure to use a heavy duty freezer safe bag or container. 

Nutrition Information

Nutrition Facts
Amount per Serving
Where does nutrition info come from? Nutrition facts are provided as a courtesy, sourced from the USDA Food Database.
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  1. 5 stars
    Thanks so much for sharing your wonderful post with us at Full Plate Thursday this week. Please keep our great state of Texas in your thoughts and prayers as we are struggling with the aftermath of Hurricane Harvey. Hope you have a good week.
    Miz Helen

  2. Nutritional yeast is something I’ll have to try soon. You’re totally right about cooking without some of the ingredients that we’re used to, it can definitely be difficult to figure out how to use some of the unfamiliar substitutes. Thanks for sharing this!

  3. So many people have issues with dairy these days. It’s nice to know that there are substitutes that are still satisfying! Happy Fiesta Friday! – Faith, Hope, Love, & Luck – Colleen

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