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Recipe for egg and cheese breakfast muffins with mushrooms and thyme {vegetarian, gluten-free}

Egg and cheese breakfast muffins

The older I get, the more I understand the importance of breakfast. Eating first thing in the morning never has come naturally to me; when I was younger, I seldom ate before noon, and even now, I usually need to work for a few hours before I can face anything more substantial than coffee. Egg and cheese breakfast muffins, made ahead and stored in the refrigerator, give me the protein boost that sees me through the day. And, like quiche or frittata, these muffins taste delicious with any mix-ins: green chiles, slow-roasted tomatoes, bell peppers, fresh herbs, smoked salmon or bacon or turkey sausage. Raid the fridge and have fun. Some day, I might learn to love breakfast. After all, I already love breakfast muffins.

Egg and cheese breakfast muffins with mushrooms and thyme

Egg and cheese breakfast muffins with mushrooms and thyme

From the pantry, you'll need: eggs, grated or shredded cheese, dried thyme leaf, kosher salt, black pepper, cooking spray.

Adapted only slightly from Kalyn's Kitchen, where you'll find many variations on diet-friendly egg muffins. Two muffins make a healthy high-protein breakfast serving. Makes 14 muffins.


6 oz roughly chopped mushrooms (white or cremini)
12 large eggs
2 cups grated or shredded cheese (I use Sargento reduced-fat shredded four-cheese Mexican blend from the supermarket; you can use any blend of Monterey Jack, cheddar, mozzarella, etc.)
2 Tbsp skim milk
1-1/2 tsp dried thyme leaf
1/2 tsp kosher salt
1/2 tsp fresh black pepper
Cooking spray


Preheat oven to 375°F. Prepare a standard 12-muffin tin and two small ramekins by spraying with cooking spray, or lining with paper muffin liners.

In a small, nonstick frying pan over low heat, cook the mushrooms until they have given up their liquid and are beginning to brown. (Do not add any fat to the pan.) Set aside to cool slightly while you prepare the remaining ingredients.

In a large bowl, whisk the eggs until smooth. Add the remaining ingredients, and whisk to combine. Stir in the cooled mushrooms.

Use a 1/3-cup measuring cup to fill the muffin tin and ramekins. (Or, make 12 muffins and cook the leftover as scrambled eggs.)

Bake for 35 minutes. The muffins will be puffed and brown on top. Remove from the oven and set aside to cool for 5 minutes before serving. The muffins will begin to collapse a bit as they cool. Or, let them cool completely and pack two-to-a-bag for the refrigerator.

[Printer-friendly recipe.]

More recipes in The Perfect Pantry:
Green chile, cheese and egg breakfast or lunch muffins
Corn, Green chile, egg and cheese casserole
Red pepper, asparagus and spinach quiche
Zucchini frittata
Oven-baked tortilla española

Other recipes that use these pantry ingredients:
Cottage cheese and egg breakfast muffins with ham and cheddar, from Kalyn's Kitchen
Herb-baked eggs, from A Bloggable Life
Smoked salmon egg casserole with potatoes and dill, from Cookin' Canuck
Spinach and mushroom frittata, from Cooking.. by the Seat of My Pants!
Spicy baked egg muffins, from Lisa's Kitchen

Disclosure: The Perfect Pantry earns a few pennies on purchases made through the Amazon.com links in this post. Thank you for supporting this site when you start your shopping here.


I'm the same way, I can't eat for at least an hour after I wake up, but coffee right away is a must! These would also be really good with shiitake mushrooms, and a sprinkle of rosemary.

These are perfect for breakfast or a light lunch Lydia!!

Those look fabulous, Lydia! I like breakfast, but I don't usually eat it first thing ... have to dilly dally a bit. ;-) I will definitely make these breakfast muffins of yours. Hubby will love them because they include mushrooms. :-)

Ok I am the weirdo here but I wake up starving!!
But in high school it was only diet coke before noon and in college it was only a hangover before noon. Now as a married, working girl I kick-start my day with a rather heavy breakfast and a light lunch. It works for me but most people think I am weird.
love these "muffins"

Brittany, I think any mushrooms and spices would be delicious here. It's fun to use what you have on hand.

Bellini, yes, either one. I do like them for lunch, too.

Shirley, glad to know there are other "breakfast procrastinators" out there.

Carol, sometimes, by the time I get around to eating breakfast, it's more like brunch. Just takes me a while to get "ready", I guess.

I like to use diced feta cheese in these and they freeze beautifully. Sometime I make them in an 8" square pan and put a tomato slice on top of each serving.

Now that I work at home I'm getting quite bad at managing breakfast myself. I used to do better when I had to get out the door; then I knew if I didn't eat breakfast it was nothing until noon!

Love the idea of adding some thyme to the mushrooms in these; one of my favorite flavor combos!

What a fantastic idea, Lydia! I think I will make these this weekend - I have a lot of eggs from our farm buying club, and this would be a great way to use them. Do you heat the refrigerated muffins before eating?

Francine, feta sounds delicious and would give these a lovely tangy flavor.

Kalyn, I feel about thyme the way you feel about cilantro. Love it in everything.

Judy, I usually reheat the muffins in a microwave for just a minute or so to take the chill off, but I've been known to eat them cold, too.

What a nice way to start the day! I would love to have something like this every morning.

hey lydia. does the muffin rise without baking soda??

DRT, it's a great way to start the day.

Aarti, the muffins puff up a bit in the oven, like any baked egg dish will do, but then they start to collapse a little bit when they cool. More like a souffle than a cake, in terms of rising.

Yet another breakfast procrastinator here, lol. But, these look fantastic - perfect for brunch.

Yet another breakfast procrastinator here, but one of my New Year's resolutions has been to include a "decent" breakfast in my day before I leave the house :). I've actually being doing it and have noticed better productivity at work!

Do you think these would freeze well?

Jessica, you can freeze these, but they need to be reheated in the oven rather than the microwave, which makes them a bit mushy. Better to keep them in the refrigerator; then, you can microwave to reheat.

These look delicious. From my reading I learned how important breakfast is. It literally breaks the fast from overnight. A nutritionist explained that it started the metabalism going. Like many fat folks - I would skip breakfast, get busy and sometimes not eat until noon or later. Not good.
I've found expanding my idea of breakfast has helped me. If I'm rushing - a handful of nuts and an apple is breakfast. I have also had sardines on top of a tomato as well as soup for breakfast. Other times oatmeal, half a pb&j or even a boiled egg are the ticket. This is really helping me eat more sensibly throughout the day. Every other weekend, I do the works - a big breakfast. Anyhow...today is the day for a big breakfast I think. Gotta run.

I've made variations of these often - they're always so good. These look like they're no exception! Yum.

GREAT! Idea, thank you

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