A healthy breakfast packed in a mug Egg Muffins with mushrooms and goat cheese. Customization options to create these Recipes for egg muffins all your own and easy freezing options!

Few things are better than having a ready-made, easy breakfast recipe that you can enjoy first thing in the morning… right? These egg muffins can be made ahead of time and reheated during the day (or eat them cold, no prejudice!) for a satisfying start to the day.
These Breakfast Egg Muffins have had a few rounds of testing, but now that the recipe is perfected I can’t wait to share!
Here’s what you need
- eggs – normal old eggs! I’ve tried this with egg whites and it didn’t work out so use the whole egg!
- goat cheese – You can omit the cheese to make it non-dairy or replace it with another cheese you have on hand if needed eg Cheddar cheese, Parmesan cheese, Monterey Jack
- Yellow Onion – gives these egg muffins the perfect savory flavor.
- Mushrooms – one of the stars! Any type of mushroom will work, but I prefer baby bellas for this recipe.
- milk [any kind] – Any kind of milk will work, but I use unsweetened almond milk because I usually have it on hand.
- Dried Thyme – You mix just a touch of spice into the vegetable mixture before adding the eggs. Feel free to substitute with fresh thyme if you have it!
- salt and pepper – taste good!
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 peppers – Sauté chopped red peppers and add your spinach a few minutes before cooking to wilt the greens.
- Ham and cheese – Any meat really works! Add chopped ham, bacon, breakfast sausage, etc. and cheese to the muffin tin for an extra protein boost.
- broccoli and cheese – Get your greens first thing in the morning! I recommend sautéing or steaming the broccoli before adding the cheese and egg mixture.
- Kale and Mushroom – Add a bit of onion or garlic to this veggie combo and you have a veggie flavor blast! Fry all the vegetables to soften them before baking with the egg mixture.
- Tomato, pepper and spinach – Another flavorful vegetarian option. Fry the chopped peppers with the chopped tomato and add the spinach just before cooking to wilt it a bit.
How to make egg muffins
STEP 1: Heat olive oil in a large skillet over medium-high heat. Add onions and sauté until translucent. Add the mushrooms and sauté another 5 minutes or until the mushrooms are cooked through.

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

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

STEP 4: Grease a muffin tin well and place about 1 tablespoon of the onion and mushroom mixture into each cup.

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

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

STEP 7: Run a knife around the edges of each muffin pan until the egg muffins loosen and pop out easily.

How to serve egg muffins
These little egg muffin cases could be a meal in themselves! If you want something to pair it with, or are doing 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 upgraded with a side dish of fruit!
- breakfast meat – Pair it with bacon, breakfast sausage, or tempeh sausage for extra protein.
- side salad – Call me weird, but I love having a side salad with egg dishes for breakfast. Get your greens early in the day!
Tips for preventing sticking
nonstick spray or butter– Always (and I mean ALWAYS) grease your egg muffin pan with either non-stick cooking spray (I like to spray olive oil) or use butter and brush it super well. You want to get the bottom, sides, and just the top.
parchment paper – I find that despite my best efforts, egg muffins still stick a little. For added dimension, I like to cut circles out of parchment paper to place in the bottom of each muffin pan. I find this method the best as filling the whole cup with parchment paper can result in a misshapen egg cup.
Silicone muffin cups– I would not recommend regular paper liners as they tend to stick to the egg, but you can use silicone muffin liners, which are easy to peel off and reusable.
How to store leftovers
In the refrigerator – These egg muffins store super well! Once cool on a wire rack, refrigerate in an airtight container for up to 1 week. Simply heat in the microwave for about 30 seconds. Perfect for meal prep!
Freeze- Let the muffins cool completely, then wrap them individually in plastic wrap or aluminum foil. Place them in a ziplock bag and freeze them for up to 3 months. Thaw overnight in the fridge or reheat straight from the freezer.
More egg recipes:
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Egg muffins with mushrooms and goat cheese
A healthy breakfast in a mug with these Mushroom Goat Cheese Egg Muffins. Customization options to make all this your own and easy freezing options!
- Preparation time: 15 minutes
- Cooking time: 15 minutes
- Total time: 30 minutes
- Yield: 12 Egg Muffins 1X
- Category: Breakfast
- Method: Cook
- Diet: Gluten free
- 1 teaspoon olive oil
- 1/2 cup yellow onion, chopped
- 8 ounces sliced ​​mushrooms, chopped
- 1/2 tsp dried thyme
- 1/4 cup goat cheese
- 9 Big Eggs
- 1/3 cup milk (any kind will do)
- 1/2 tsp sea-salt
- Freshly ground black pepper to taste
- Preheat oven to 375 degrees F.
- In a large pan, heat olive oil over medium-high heat.
- Add onions and sauté until translucent (about 3 minutes)
- Add mushrooms and sauté another 5 minutes or until mushrooms are cooked through.
- Turn off the heat and add the thyme and goat cheese and mix until well combined.
- In a separate bowl, whisk eggs and milk. Add sea salt.
- Grease a muffin tin VERY well (and optionally add circles of parchment as shown above) and spoon about 1 tablespoon of the onion and mushroom mixture into all 12 cups.
- Top up with the egg and milk mixture until each cup is full and sprinkle each cup with pepper.
- Bake egg muffins for 13-15 minutes or until egg is set.
- Remove from the oven and let cool for 20 minutes.
- Run a knife around the edges until the frittatas loosen and are easy to remove.
- Lasts up to 1 week in the fridge or 3 months in the freezer (see storage instructions above)
Keywords: Egg Muffins, Egg Cups, Mini Frittatas, Mushroom Egg Muffins, Egg Muffin Recipes

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