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A healthy breakfast packed all into one cup with these egg muffins with mushrooms and goat cheese. Customization options to make these egg muffin recipes all your own and easy freeze options too!

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Few things are better than having a pre-made easy breakfast recipe ready to indulge in first thing in the morning… amiright? These egg muffins can be made ahead of time and heated up the day of (or eat them cold, no judgement!) for a satisfying way to start your day. 

These breakfast egg muffins took a few rounds of testing but now that the recipe is perfected, I can’t wait to share!

Here’s What You Need

  • Eggs – just regular ol’ eggs! I tried this with egg whites and it didn’t turn out so use the full egg!
  • Goat cheese – you can omit the cheese to make it dairy-free or swap for a different cheese you have on hand if needed e.g. cheddar cheese, parmesan cheese, monterey jack
  • Yellow onion – adds the perfect savory flavor to these egg muffins.
  • Mushrooms – one of the stars! Any type of mushroom works but I prefer baby bellas for this recipe.
  • Milk [any kind] – any type of milk works but I use unsweetened almond milk because that’s what I usually have on hand.
  • Dried thyme – you’ll mix in just a hint of seasoning to the vegetable mixture before adding in the eggs. Feel free to sub with fresh thyme if you have it!
  • Salt and pepper – to taste!

Flavor Variations

I love the flavor of these egg muffins but this recipe is completely customizable! Here are some ideas for different egg muffin recipes:

  • Spinach and red pepper – Sauté chopped red pepper and add in your spinach a few minutes before you’re done cooking to wilt the greens.  
  • Ham and cheese – Any meat works really! Add chopped ham, bacon, breakfast sausage, etc. and cheese to the muffin tin for an extra boost of protein. 
  • Broccoli and cheese – Get your greens in first thing in the morning! I recommend sautéing or steaming your broccoli before adding the cheese and egg mixture. 
  • Kale and mushroom – Add a little onion or garlic to this veggie combination and you have a vegetarian flavor explosion! Sauté all of the veggies to soften before baking with egg mixture. 
  • Tomato, pepper and spinach – Another flavor packed vegetarian option. Sauté chopped bell peppers with the chopped tomato and then add in the spinach right before you’re done cooking so it can wilt a bit. 

How to Make Egg Muffins

STEP 1: Heat olive oil in a large skillet over medium heat. Add onions and sauté until translucent. Add in the mushrooms and sauté for another 5 minutes or until mushrooms are cooked. 

STEP 2: Turn off the heat and stir in the goat cheese and thyme. Mix until well combined. 

STEP 3: In a large bowl, whisk the eggs and milk. Season with salt and pepper. 

STEP 4: Grease a muffin pan really well and add roughly 1 tablespoon of the onion-mushroom mixture to each cup. 

STEP 5: Top each muffin cup with the egg mixture until cup is full. 

STEP 6: Bake at 375ºF for 13-15 minutes or until the egg has set. Remove from the oven and let cool for 20 minutes.

STEP 7: Run a knife around the edges of each muffin cup until the egg muffins loosen up and are easy to remove. 

How to Serve Egg Muffins

These little egg muffin cups could be a meal on its own! If you want something to pair it with or are making this for a crowd, here are some ideas:

  • Sliced avocado – I love adding sliced avocado to pretty much any egg breakfast. 
  • Fruit salad – breakfast can always be elevated with a side of fruit!
  • Breakfast meat – pair with bacon, breakfast sausage or tempeh sausage for added protein. 
  • Side salad – call me weird but I love having a side salad with egg dishes for breakfast. Get your greens in early in the day!

Tips to Prevent Sticking

Non-stick spray or butter– always (and I mean ALWAYS) grease your egg muffin tin with either non-stick cooking spray (I like spray olive oil) or use butter and brush super well. You’ll want to get the bottom, sides and alone the top.

Parchment paper – I do find that in spite of my best efforts egg muffins will still stick a little. For extra measure I like to cut circles of parchment paper to place onto the bottom of each muffin cup. I find this method words best as filling the whole cup with parchment paper can lead to a misshapen egg cup.

Silicone muffin liners– I would not recommend regular paper liners as they tend to stick to the egg but you can use silicone muffin liners that will peel off easily and are reusable.

How to Store Leftovers

In Fridge – These egg muffins store super well! After allowing to cool on a wire rack, place in an airtight container in the refrigerator for up to 1 week. Just heat in the microwave for roughly 30 seconds. Perfect for meal prep!

To Freeze- Let the muffins cool completely, then individually wrap them in plastic wrap or tinfoil. Place them in a ziplock bag and freeze for up to 3 months. Let thaw overnight in the refrigerator or reheat directly from frozen.

More Egg Recipes: 


Egg Muffins with Mushrooms and Goat Cheese

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 3 reviews

A healthy breakfast packed all into one cup with these egg muffins with mushrooms and goat cheese. Customization options to make these all your own and easy freeze options too!

  • Author: Davida Lederle
  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Total Time: 30 minutes
  • Yield: 12 egg muffins 1x
  • Category: Breakfast
  • Method: Cook
  • Diet: Gluten Free


  • 1 tsp olive oil
  • 1/2 cup yellow onion, chopped
  • 8 oz sliced mushrooms, chopped
  • 1/2 tsp dried thyme
  • 1/4 cup goat cheese
  • 9 large eggs
  • 1/3 cup milk (any kind will work)
  • 1/2 tsp sea salt
  • Freshly ground black pepper, to taste


  1. Preheat oven to 375 degrees F.
  2. In a large pan heat olive oil over medium heat.
  3. Add onions and sauté until translucent (about 3 minutes)
  4. Add in mushrooms and saute for another 5 minutes or until mushrooms are cooked through.
  5. Turn off heat and add in thyme and goat cheese and mix until well combined.
  6. In a separate bowl whisk eggs and milk. Add in sea salt.
  7. Grease a muffin tin VERY well (and add optional parchment circles as shown above) and add roughly a tablespoon of the onion-mushroom mixture to all 12 cups.
  8. Top with egg-milk mixture until each cup is full and sprinkle each with pepper.
  9. Bake egg muffins for 13-15 minutes or until egg has set.
  10. Remove from oven and let cool for 20 minutes.
  11. Place a knife around the edges until the frittatas loosen up and are easy to remove.
  12. Will keep in fridge for up to 1 week or store in freezer for 3 months (see storage instructions above)

Meet the Maven

Hi! I'm Davida and welcome to my corner of the internet. I'm a wellness blogger, yoga teacher, certified herbalist, and green beauty lover.

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  1. So simple and yum. Really lovely taste. We had it for breakfast and planning to use as our go to Sunday breakfast.