These egg and cheese muffins are easy, frugal, protein-packed, gluten-free, and meal-prep perfection. Also – very delicious.
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Looking for a healthy breakfast on a budget that works for busy mornings, picky eaters, and even food allergies? These easy egg and cheese breakfast muffins check every box. They’re high in protein, naturally gluten-free, customizable, and perfect for meal prep or freezing ahead.
Why We Love Egg & Cheese Breakfast Muffins
Whether you’re a busy parent trying to get out the door or just trying to eat better without spending a fortune, these muffins are a breakfast game-changer.
Budget-Friendly
Eggs are inexpensive, nutritious, and easy to cook. Even if you buy the best eggs nature and farmers have to offer – free-range, local, organic, pampered chickens – a dozen eggs costs the same or less than a latte from the coffee shop. You can use the same amount of money to make a protein-packed breakfast for your whole family – or meal prep for yourself for a few days.
High Protein
Packed with protein and healthy fats, egg muffins help keep you full longer. They’re made with real, whole food ingredients—no weird powders or mystery freezer meals required. They are also keto-friendly, grain-free, and gluten-free.
Meal-Prep
These egg & cheese muffins are the perfect easy, homemade, protein-packed, on-the-go breakfasts – ideal for making ahead, freezing, reheating, eating fresh (or even cold).
We make a batch of these at the beginning of the week, and we eat them for breakfast the next few days. Or we use them for packed lunches, meatless dinners, or a filling mid-afternoon snack.
Easy Egg & Cheese Muffins
Scrambled eggs are easy enough to make, but what if you only have a few minutes to whip something together for the family? Or you are trying to maximize your meal prepping time? Egg and cheese muffins take about 5 minutes to stir together and pop in the oven.
They aren’t just scrambled eggs poured into muffin liners. The parmesan cheese makes them savory and filling enough for lunch or dinner, but still very budget-friendly.
Easy Egg & Cheese Muffins
These egg and cheese muffins are easy, frugal, protein-packed, gluten-free, and meal-prep perfection. Also - very delicious.
Ingredients
- 12 eggs
- 2 cups cheddar cheese, shredded
- 1 cup parmesan cheese, shredded
- 1/4 tsp oregano
- 1/4 tsp basil
- 1/2 tsp salt, to taste
- 1/4 tsp pepper, to taste
Optional (Choose 1 or 2):
- 1-2 cups peppers and onions, diced and sautéed
- 1-2 cups chopped spinach (fresh or frozen and thawed)
- 1-2 cups breakfast sausage, crumbled
- 1 cup bacon, crumbled
- 1 cup turkey bacon, crumbled
Instructions
- Preheat the oven to 350°F.
- Line a muffin pan with paper liners (I don’t recommend skipping the liners – these babies stick to the pan) and lightly grease the liners and the top of the pan to prevent the puffy muffin tops from sticking to the edges.
- Combine all ingredients in a bowl, whisking thoroughly.
- Distribute the batter evenly between the 12 muffin cups.
- Bake for 20-25 minutes, until the tops are golden brown and the egg is cooked through.
- Allow to cool for 10 minutes before removing from the pan and enjoying.
Notes
Cheese:
If you have any leftover shredded cheese or bits that need to be used up, this recipe is the perfect way to use them.
Frittata Version:
Pour the egg batter into a greased baking dish and bake for 20-30 minutes.
Nutrition Information
Yield 12 Serving Size 1 muffinAmount Per Serving Calories 422Total Fat 31gSaturated Fat 12gTrans Fat 0gUnsaturated Fat 17gCholesterol 277mgSodium 1338mgCarbohydrates 6gFiber 1gSugar 3gProtein 29g
Please note: The actual calories and nutrition of this dish will change depending on what ingredients you use. Nutrition information is not always accurate.
What to Serve with Egg & Cheese Muffins
Make a complete meal with these sides:
- Seasonal fruit
- Sautéed veggies
- Baked Oatmeal
- Whole Wheat Muffins
- Smoothie
Freezing & Storing Tips
Perfect your meal-prepping game with these storage tips.
Refrigerate
Store the egg and cheese muffins in the fridge in a sealed container for 3-4 days.
How to Freeze
Let the egg and cheese muffins cool completely (preferably in the fridge overnight), then either double bag them in freezer bags or wrap them in plastic wrap and then store them in a freezer bag. The goal is to limit the amount the air around the muffins while they sit in the freezer. Label the bag with the contents and date. You can store these muffins for up to 6 months, but they taste best if you use them within 3 months.
Reheating Instructions
These muffins reheat well in the microwave. If you don’t have a microwave, try this hack: dunk them under running water for just one second, place them on a baking sheet, and reheat them in an oven or toaster oven for 15-20 minutes at 400 F.
Tips & Variations
Make this recipe work for you by trying these different flavors and cooking methods.
Egg & Cheese Muffin Flavor Variations
The muffins are really delicious and savory. However, if you want to try something different, add one or two of these to the egg batter:
- Sautéed veggies
- Crumbled breakfast sausage (try this 5-ingredient homemade!)
- Bacon bits
- Turkey bacon bits
- Different kinds of shredded cheese
No Muffin Tin?
If making muffins is too fussy (FACT: muffin-shaped food always tastes more delicious), just pour the egg and cheese batter into a greased baking dish. I honestly prefer this method, because it’s easier, and the egg doesn’t stick to the liners.
If you use a baking dish, it’s more of a frittata than anything else. But that’s delicious too, so I’m not complaining.
More Breakfast Inspiration:
- Allergy-free Baked Oatmeal (no weird ingredients!)
- Breakfast Apple Crisp
- Easy Vegetable Frittata
- Overnight Oats for a Crowd
- Sneaky Veggie Baked Oatmeal
Final Thoughts
These easy egg and cheese breakfast muffins are a lifesaver for busy families who want to eat healthy and save money. They’re easy to make, easy to store, and easy to customize for food allergies or picky eaters.
Add them to your next meal prep session, and enjoy healthy, affordable breakfasts all week long.
Have you made these muffins? Drop a comment below and let us know how it turned out—or tag @cheapskatecook on Instagram.
I love these! They are so good. Especially with a hot cup of coffee.
Made these today! They are so delicious! What a super simple recipe.
Yay! I’m glad you like them!
We’ve made two versions now with bacon and cheddar, and ham and Swiss. Big hits! I knocked a few minutes off the cook time because mine were a little rubbery the first time. I’m putting these and your baked oatmeal in my “make once a week” rotation. Super easy to reheat for busy mornings. Thank you!
Awesome, Nicole! Glad you were able to make it your own – and that they made your weekly rotation. That’s a huge compliment!
Fyi, we dont like eggs frozen and reheated, theyve got a weird sponge like texture. So make this and stick just a few in the freezer to try. You may be lucky and like them but you wont waste a whole recipe if you dont. They ARE edible, just not at all enjoyable. I cant do make ahead quiche, egg bakes, scrambled eggs, anything beyond frizen breakfast burritos as the tortilla masks the spongey texture…and theres not much egg in it anyway lol
Yep, always try something first. We like these reheated eggs just fine – maybe because there is plenty of cheese in them!
I’m super excited to try these! I don’t have time to
make a fresh batch daily so I’m looking forward to prepping and eating for the week! Thanks so much for the idea!
Awesome, Heather! I’m so happy!
I have to try these! Sounds delicious!
This is one of my favorite delicious make-ahead recipes… making this right now.
I’m so glad! They are SO delicious.
5 stars all the way! Really delicious! I had to cook for additional time. However, every oven is different. Thank you so much for sharing.
I started using the parchment liners for muffins and such, if you cant find them(Target Only for us so far) you can cut parchment into squares to fit your muffin tin then they won’t stick. Thank you for another wonderful affordable recipe that we can customize.
Love this easy recipe and I make it in a square Pyrex dish – so much easier than fiddling with muffin tins in my opinion.
Add whatever I might need to use up that’s sitting in my fridge. Great accompaniment to a fresh green salad ! Thank you.
Hi Bobbi! I’ve thought of adding an update to the recipe with the baking dish version because I love that too! I agree, so easy and delicious. Thanks for the comment!
Hi!
What size baking dish please? And…do you bake for the same amount of time?
Hi Denise! I would use an 8×8 inch pan and start with the baking time on the recipe, then check it and add more if necessary (just 5 min at a time)
Hi! These muffins were delicious, but they completely stuck to the muffin liners! I also added cream and ham to make them outstanding!
Hi Viv! That’s so frustrating! Sometimes spraying the liners helps. I also like to bake it in a baking dish when I don’t have good muffin liners on hand (don’t forget to spray tho!).
Made these today. I had a lot of leftover mixture. I’m afraid I’ve done something wrong. I used regular size muffin tins (12). Could it be because I added sausage?
Hi Paula!
Yes, I think adding the sausage increased how much egg mixture you had!
Delish! My favorite egg muffin recipe.
Did not have a problem with eggs sticking to muffin liners
I omitted the salt and pepper; i used a little Herbes de Provence instead.
I used reduced pkg sharp cheddar and it melted in the eggs very well.
Thank you for recipe ❤️
I think spraying the muffin tin with Baker’s Joy (or any oil/flour spray) would prevent the egg mixture from sticking. I do this with cornbread and it never sticks.