Cottage Cheese Egg Muffins are an easy, mostly hands-off, high protein breakfast. The cottage cheese melts and turns into ooey-gooey pockets of cheese.
It's quickly become one of my favorite ways to use up cottage cheese, as well as sneak extra protein in during the day. Serve these delicious egg muffins for breakfast, brunch, or an after-workout snack.
Jump to Recipe
As an Amazon Associate, I earn from qualifying purchases. This post contains affiliate links for products I use and love. You can read my full disclosure here. All thoughts and opinions expressed are my own. Thank you for supporting Wonders of Cooking so that I can continue to provide you with free gluten-free recipes.
Looking for More Breakfast Recipes?
- Gluten Free Sourdough Poptarts Recipe | Brown Sugar and Cinnamon
- Gluten Free Sourdough Poptarts | Homemade Strawberry Poptarts
- Best Gluten Free Peach Bread | Gluten Free Peach Recipes
- Gluten Free Banana Bread Muffins - Banana Nut Muffins (One Bowl)
- Easy Breakfast Casserole | Sausage, Egg, and Cheese
- Creamy Orange Smoothie | Easy Healthy Breakfast
- Five Ingredient Banana Oat Pancakes | Flourless, Dairy Free

Tips for Making the Best Cottage Cheese Egg Muffins:
- Precook the sausage, crumbled bacon, etc. before baking the egg muffins. This ensures the meat cooks through and browns, as well as allows you to drain any grease.
- Use full fat cottage cheese. Low fat cottage cheese produces too much liquid while baking.
- If adding in vegetables, stick to veggies that don't produce much water. I recommend potatoes (precooked), bell peppers, onion, and broccoli. You may want to precook mushrooms, spinach, etc.
- Be sure to use baking powder to make the fluffiest egg muffins possible. This trick really prevents them from being dense. Seriously, these are the fluffiest egg muffins I've ever had!
- Use gluten-free or regular all purpose flour. This also adds an extra touch to the egg muffins, preventing them from being dense. You won't notice the taste of flour in the finished product.
- Use chives, green onion, and your favorite seasonings like sun dried tomatoes, thyme, and oregano.

Ingredients for Cottage Cheese Egg Bites:
- Full fat cottage cheese
- Large eggs
- Shredded cheddar cheese
- Crumbled breakfast sausage
- Chives
- Gluten-free all purpose flour, or regular all purpose. I use Bob's Red Mill GF 1:1 Baking Flour
- Baking Powder
- Salt & pepper

Cottage Cheese Egg Muffins Recipe:
- Preheat the oven to 350 F. Grease two muffin trays with some butter or nonstick cooking spray, or use a silicone cupcake tray or muffin liners. (Recipe makes about 18 standard muffins.)
- Brown the sausage over medium-high heat on the stove-top, crumbling as it cooks, until cooked through. Drain excess grease.
- Meanwhile, add the eggs to a large mixing bowl. Tip: Use a bowl that has a pouring spout if you have one. Whisk until smooth.
- Add in the cottage cheese, shredded cheddar cheese, chives, salt, and pepper. Whisk until incorporated.
- Sift the flour and baking powder over the mixture, and whisk until just combined.
- To assemble: Evenly spoon the crumbled and drained sausage into the bottoms of the prepared muffin trays. Pour the egg batter over top of the sausage, filling each cavity ¾ of the way full.
- Place the muffin trays on a cookie sheet to catch any spills while baking. Then, place on the middle rack of the oven, and bake for 30-35 minutes. Test the center's with a thermometer. It should read at-least 160 F. Tip: The cottage cheese will melt into gooey pockets. I like to use a thermometer to ensure it's not under-cooked whites.
- Remove from the oven and set aside to cool for 10-15 minutes in the pan before serving.
- Once cooled, store in an airtight container in the refrigerator. Enjoy within 3 to 4 days.
Equipment
You only need basic tools to make Cottage Cheese Egg Muffins. I recommend:
- A whisk is helpful in this recipe.
- A large sheet pan to catch the drips
- Parchment paper makes cleanup a breeze.
- Silicone Muffin Tray
- Silicone Baking Mat
- Digital Thermometer

How to Store Cottage Cheese Egg Muffins:
You can store cottage cheese egg bites in an airtight container in the refrigerator for three to four days. They make excellent meal prep!
To reheat: Place the desired amount of egg bites on a plate. Cover with a wet paper towel. Microwave for 45-60 seconds, until warm and fluffy. They will be dense straight from the fridge, but the microwave will make them soft and bouncy again. (I totally eat three muffins per serving.)
Tried this Cottage Cheese Egg Muffins Recipe? Leave a 5-Star Rating Below!

Cottage Cheese Egg Muffins | Best High Protein Cottage Cheese Recipes
Your rating helps support the making of more tested, delicious gluten-free recipes.
Ingredients
- 12 large eggs
- 2 cups full fat cottage cheese
- 1 cup shredded cheddar cheese
- 16 oz. breakfast sausage roll (1 lb)
- 4 tablespoon gluten-free all purpose flour or regular flour
- 2 tablespoon chives
- 1 teaspoon baking powder
- ¼ teaspoon salt
- black pepper to taste
Instructions
- Preheat the oven to 350 F. Grease two muffin trays with some butter or nonstick cooking spray, or use a silicone cupcake tray or muffin liners.
- Brown the sausage over medium-high heat on the stove-top, crumbling as it cooks, until cooked through. Drain excess grease.16 oz. breakfast sausage roll
- Meanwhile, add the eggs to a large mixing bowl. Tip: Use a bowl that has a pouring spout if you have one. Whisk until smooth.12 large eggs
- Add in the cottage cheese, shredded cheddar cheese, chives, salt, and pepper. Whisk until incorporated.2 cups full fat cottage cheese, 1 cup shredded cheddar cheese, 2 tablespoon chives, ¼ teaspoon salt, black pepper to taste
- Sift the flour and baking powder over the mixture, and whisk until just combined.To assemble: Evenly spoon the crumbled and drained sausage into the bottoms of the prepared muffin trays. Pour the egg batter over top of the sausage, filling each cavity ¾ of the way full.4 tablespoon gluten-free all purpose flour, 1 teaspoon baking powder
- Place the muffin trays on a cookie sheet to catch any spills while baking. Then, place on the middle rack of the oven, and bake for 30-35 minutes. Test the center's with a thermometer. It should read at-least 160 F. Tip: The cottage cheese will melt into gooey pockets. I like to use a thermometer to ensure it's not under-cooked whites.
- Remove from the oven and set aside to cool for 10-15 minutes in the pan before serving.
- Once cooled, store in an airtight container in the refrigerator. Enjoy within 3 to 4 days.
Leave a Reply