Keto Cottage Cheese Brookie Muffins
If a brownie, a cookie, and a muffin had a high-protein baby, and it tasted like chocolate peanut butter, these keto cottage cheese brookies muffins would be it. Each keto brookie is baked in a mini muffin tin with a soft, fudgy base and a golden cookie top – no shaping, slicing, or refined sugar. You get the best of all three: gooey brownie texture, cookie flavor, and muffin-style portion control.
Each of the gluten-free cottage cheese brownies is naturally portioned, made with real, simple ingredients, yet soft and indulgent.
Each one has 5.2 grams of protein and just 2.8 net carbs. The texture? All soft and gooey. The protein boost? Straight from cottage cheese, not protein powders or fillers.
These dangerously good protein brookies bake in 20 minutes and come out rich, warm, and ready to stash or serve.
These low carb brownie cookies are a real win when you want a sugar-free treat but not the mess of shaping cookies or the sugar crash of traditional bakes.
Because sometimes you want a treat, not a tray of cleanup.
These Cottage Cheese Brookies Are
- For when you want something gooey, sweet, and portioned without lots of carbs
- Baked in a muffin tray because shaping cookies at 9 p.m. is not the vibe
- Made with real ingredients like cottage cheese and peanut butter for a soft, rich texture
- Different from regular brookies or cookies because they are made in a muffin tin for portion control and ease.
- A smarter swap for skillet brookies that are harder to portion and store
- These are not for everyone! Not for you if you’re after crispy cookie edges or a dry, classic cookie texture. These stay soft and fudgy, just how we like them
Watch how I make this in minutes! It’s like we’re cooking side-by-side in my kitchen!
Instructions
- Preheat oven to 350°F (175°C) and grease a mini muffin tray or line with silicone cups.
- For the brownie base, blend in a blender or food processor the wet ingredients: cottage cheese, peanut butter, egg, sweetener, and vanilla until smooth. Then add the dry ingredients: cocoa powder, almond flour, and baking powder, and blend again until thick and pourable.
- Fold in the chocolate chips, then use a small cookie scoop to portion the batter into the muffin tray – about 3/4 full per cup.
- For the cookie layer, blend cottage cheese, coconut flour and sweetener until thick and creamy.
- Use a teaspoon (or your fingers) to gently spread a little cookie batter over each brownie base – no need to shape, swirl, or make it perfect.
- Bake for 20 minutes until the tops look set and lightly golden, then let them cool fully in the tray so the brownie base sets up.
Testing Notes
I tested this recipe using different pans and methods and here’s what I found:
- Muffin tins gave the best results every time. The brownie base stayed gooey and soft without falling apart, and the cookie top baked up golden and set without drying out.
- Skillet versions were harder to portion and overcooked at the edges.
- Trying to shape the brownie batter into cookies was a fail. It’s pourable, not doughy. Most recipes skip this detail, but it makes a big difference.
Using a muffin tray solved everything – no fuss, no shaping, and way more fudginess in every bite.
Ingredient Swaps
- If you’re out of cottage cheese, you can use full-fat Greek yogurt for the cookie layer. It’ll bake up a little fluffier and less tangy, but the protein will drop and the top might not get as golden.
- Need to go nut free? Swap the almond flour in the brownie base for 1 tablespoon of coconut flour. You may need to add extra liquid.
- Prefer a swirl? You can totally swirl the cookie layer into the brownie base before baking.
Storage Tips
- Fridge: Store these in an airtight container for up to 5 days. They’ll stay soft and fudgy, and you can eat them straight from the fridge or let them come to room temperature if you want that gooey center back.
- Freezer: Freeze in a single layer first so they don’t stick together, then toss them in a freezer bag or container. Reheat gently in the microwave or oven, just enough to warm the center, not dry them out.
Make It a Moment
Warm one of these brookie muffins and serve it with a scoop of vanilla ice cream or a spoonful of whipped cottage cheese for that warm-meets-cold contrast. Want to double the chocolate but change the texture? Pair it with a quick chocolate cottage cheese mousse – soft, spoonable, and ready in minutes.
Conclusion
This has become my go-to when I want something sweet without the mess or the stress. No shaping, no scooping, no guessing if the center will bake through. The brownie stays fudgy, the cookie top turns golden, and each one has enough protein to actually hit the spot.
If you miss real desserts but not the sugar crash, this one’s worth keeping on hand. They freeze well, reheat fast, and feel like a treat without turning into a whole production.
FAQ
Can I make a skillet version?
You can. Use an 8-inch oven-safe skillet and bake for 18 to 22 minutes.
Can I double the recipe?
Yep. The base recipe makes 6, so if your muffin tray holds 12, you’re already set. Just hit “2x” in the recipe card to scale it up, and expect to add a few extra minutes to the bake time.
Do they freeze well?
Yes. Freeze them in a single layer first, then place them into a container or bag once solid. They’re perfect for meal prep. Just grab one when you want something sweet, and reheat gently in the microwave or oven until warm and soft again.
More Recipes
More Brownie-Inspired Recipes
More Cookie-Style Bakes
- Chocolate Chip Cookies
- Lemon Sugar Cookies
- 30+ Cottage Cheese Dessert Recipe Collection to Choose From
Cottage Cheese Brookies – Fudgy Brownie Cookie Muffins
Equipment
Ingredients
Brownie Layer
- 1/4 cup (60 ml) full-fat cottage cheese
- 2 tablespoons smooth peanut butter (natural, 100%, sugar free)
- 1/4 cup (60 ml) Swerve (granulated)
- 1 teaspoon Vanilla extract – sugar free
- 1 large egg
- 3 tablespoons almond flour
- 1/4 teaspoon (¼ teaspoon) baking powder
- 2 tablespoons cocoa powder – unsweetened
- 2 tablespoons Lily's Dark Chocolate Chips
Cookie Layer
- 2 tablespoons full-fat cottage cheese
- 1 tablespoon coconut flour
- 1 tablespoon Swerve (granulated)
Watch the Video Instructions
Instructions
- Preheat oven to 350°F (175°C) and grease a mini muffin tray or line with silicone cups.
- For the brownie base, blend in a blender or food processor the wet ingredients: cottage cheese, peanut butter, egg, sweetener, and vanilla until smooth. Then add the dry ingredients: cocoa powder, almond flour, and baking powder, and blend again until thick and pourable.1/4 cup full-fat cottage cheese, 2 tablespoons smooth peanut butter (natural, 100%, sugar free), 1/4 cup Swerve (granulated), 1 teaspoon Vanilla extract – sugar free, 1 large egg, 3 tablespoons almond flour, 1/4 teaspoon baking powder, 2 tablespoons cocoa powder – unsweetened
- Fold in the chocolate chips, then use a small cookie scoop to portion the batter into the muffin tray – about 3/4 full per cup.2 tablespoons Lily's Dark Chocolate Chips
- For the cookie layer, blend cottage cheese, coconut flour and sweetener until thick and creamy.2 tablespoons full-fat cottage cheese, 1 tablespoon coconut flour, 1 tablespoon Swerve (granulated)
- Use a teaspoon (or your fingers) to gently spread a little cookie batter over each brownie base – no need to shape, swirl, or make it perfect.
- Bake for 20 minutes until the tops look set and lightly golden, then let them cool fully in the tray so the brownie base sets up.
Notes
- Use full-fat cottage cheese for the best texture.
- Store in fridge up to 5 days or freeze for longer.
- For gooey centers, slightly underbake by 1-2 minutes.
- Add extra chocolate chips or nuts if desired.
- Great for breakfast, snack, or dessert.
Nutrition Per 1 (ONE) Serving
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These were such a fun twist on classic desserts! Super fudgy texture. Loved that they’re low carb and high protein. Will definitely be making another batch soon!