
This protein-packed cottage cheese muffin recipe transforms breakfast into something special. With a perfect balance of savory cheese and bright herbs, these muffins provide the satisfying comfort of traditional baked goods while offering significantly more nutrition. They've become my go-to for meal prep breakfasts, quick snacks, and even light lunches paired with soup.
I created this recipe during a busy work week when I needed portable breakfasts that would actually keep me full until lunch. Now they've become a staple in our household with endless variations depending on what herbs and cheese we have available.
Ingredients
- Cottage cheese: Creates moisture and adds significant protein these muffins stay tender for days
- Almond flour: Provides a nutty flavor and creates a texture that's lighter than traditional wheat flour
- Cheddar cheese: Adds rich flavor and creates those irresistible crispy edges look for aged cheddar for maximum flavor
- Fresh chives: Bring brightness and color use scissors to cut them directly into your bowl
- Ground turmeric: Offers a gorgeous golden color and subtle earthy notes plus anti inflammatory benefits
- Ground flax: Adds fiber and helps bind the mixture you can substitute more almond flour if needed
Step-by-Step Instructions
- Prepare the almond flour:
- Toast almond flour in 350°F oven for 7 to 8 minutes until it develops a light golden color and nutty aroma. This step deepens the flavor tremendously and removes any raw taste. Allow to cool completely before using.
- Prepare the muffin tin:
- Line a 12 cavity muffin tin with silicone liners or generously grease each cup. Increase oven temperature to 400°F for the perfect muffin rise and golden tops.
- Mix wet ingredients:
- Whisk eggs milk cottage cheese and olive oil until completely combined with no visible egg streaks. The mixture should look slightly curdled due to the cottage cheese texture.
- Add seasonings:
- Incorporate turmeric salt pepper and baking powder whisking vigorously to ensure the baking powder is evenly distributed. Fold in the fresh chives allowing their flavor to infuse the batter.
- Combine dry ingredients:
- Add cooled toasted almond flour and ground flax using a spatula to gently fold everything together until just combined. Overmixing will create dense muffins.
- Add cheese and bake:
- Fold in two thirds of the cheddar cheese saving the remainder for topping. Fill each muffin cup about three quarters full then sprinkle remaining cheese on top. Bake for 15 to 20 minutes until tops are golden and centers are set.

The cottage cheese is truly the star ingredient here. I discovered its magic in baking during a phase when I was trying to increase my protein intake without relying on protein powders. The cottage cheese melts into the batter creating pockets of moisture while boosting the protein content substantially.
Storage and Freezing
These muffins keep beautifully in an airtight container in the refrigerator for up to 4 days. For longer storage freeze them individually wrapped in parchment paper then placed in a freezer bag. They will maintain quality for up to 3 months. To reheat microwave for 30 seconds from refrigerated or about 1 minute from frozen. For a crispy exterior warm in a 350°F oven for 5 to 7 minutes.
Substitutions and Variations
The basic formula is incredibly adaptable to what you have on hand. Swap the cheddar for feta goat cheese or gruyere for different flavor profiles. Replace chives with any fresh herbs like dill basil or thyme. For a more substantial texture add diced red pepper caramelized onions or even cooked crumbled bacon. The almond flour can be replaced with oat flour or regular all purpose flour if gluten isn't a concern.
Serving Suggestions
While these muffins are perfect on their own for breakfast they also pair wonderfully with soups and salads for lunch. Try serving them warm with a pat of butter or split and toasted with avocado on top for an elevated avocado toast experience. For brunch serve alongside a frittata and fresh fruit for an impressive spread that comes together quickly.

These muffins make for a wholesome and satisfying start to the day — or a comforting snack anytime.
Frequently Asked Questions
- → Can I substitute the almond flour in these muffins?
Yes, you can substitute the almond flour with oat flour, all-purpose flour, or whole wheat flour in equal amounts (1¼ cups) as mentioned in the ingredients list. Each alternative will yield a slightly different texture and flavor profile.
- → How should I store these cheese muffins?
Store cooled muffins in an airtight container in the refrigerator for up to 5 days. They can also be frozen for up to 3 months. Reheat in the microwave for 20-30 seconds or in a 350°F oven for about 5-7 minutes until warmed through.
- → Are these muffins gluten-free?
When made with almond flour as specified in the recipe, these muffins are naturally gluten-free. Just ensure your baking powder is certified gluten-free if you have celiac disease or severe gluten sensitivity.
- → Can I add other herbs or vegetables to these muffins?
Absolutely! These versatile muffins work well with additions like chopped spinach, diced bell peppers, crumbled bacon, or herbs like dill or basil. Add about ¼-½ cup of additional mix-ins, being careful not to overload the batter.
- → Why toast the almond flour before using it?
Toasting the almond flour adds a deeper, nuttier flavor to the muffins and helps remove any raw taste. It also improves the texture of the final product. If you're short on time, you can skip this step, but the flavor won't be quite as rich.
- → What's the purpose of the turmeric in this recipe?
The turmeric is optional and primarily adds a beautiful golden color to the muffins. It also provides subtle earthy notes and potential anti-inflammatory benefits, but it doesn't significantly impact the overall flavor.