
Healthy keto protein muffins that taste like cinnamon rolls! These tender low carb muffins have a buttery sweet cinnamon filling and pack 11g of protein per serving.

Who doesn’t love a sweet, sticky, tender cinnamon roll? But those of us who keep our health in mind know to steer clear of these gooey breakfast pastries. We give them a wide berth, because as tasty as they are, they just aren’t worth the risk.
Thankfully, you can enjoy those same flavors in healthier ways. I have any number of recipes to enjoy, from classic keto cinnamon rolls to cinnamon roll cheesecakes. And these Cinnamon Roll Protein Muffins are my new favorite way to indulge!
I’ve been eating them daily before my workouts and they are a sweet way to start my day. It’s a wonderful high protein breakfast recipe.

Why you’ll love these muffins
If you’re going to enjoy a cinnamon roll flavored treat, why not make it work a little harder for you and pack it full of protein too? Made with cottage cheese and protein powder, these muffins have 11g grams of protein and less than 5g of carbs per serving.
They really are delicious. The muffin is tender and the cinnamon filling is sweet and buttery. The glaze on top is entirely optional and not even necessary, in my opinion. Although it does make them look make them look more like real cinnamon rolls!
And these keto protein muffins are easy to make, too. Whip the batter up in a blender, swirl in the cinnamon filling, and bake them up. Before long, you are enjoying low carb, high protein cinnamon roll goodness!
Ingredients you need

- Butter: You want the butter softened, almost melted, prior to mixing.
- Sweetener: The filling works best with a combination of brown sugar substitute and some allulose so it stays gooier. You will want a powdered sweetener if you choose to add the glaze.
- Ground cinnamon: You can’t make cinnamon rolls without cinnamon! Make sure yours is fresh, as old spices lose their flavor over time.
- Cottage cheese: I used whole milk cottage cheese but 2% should work just as well.
- Eggs: Use large eggs and make sure they are room temperature.
- Almond flour: Use blanched, finely ground almond flour for keto muffin recipes like this one.
- Protein powder: I used unflavored whey protein for this recipe. Egg white may work as well but I don’t recommend plant protein or collagen protein.
- Pantry staples: Heavy cream, vanilla extract, baking powder and salt.
Step by step directions

1. Make the cinnamon swirl: In a medium bowl, stir together the butter, sweeteners, and cinnamon. The butter should be almost melted but not quite, and the mixture should be like a thin paste. Set aside.
2. Prepare the muffin batter: In a blender, combine the cottage cheese, eggs, sweetener, and vanilla, and blend until smooth. Add the almond flour, whey protein, baking powder, and salt and blend again until smooth.
3. Assemble the muffins: Line the wells of two muffin pans with silicone or parchment liners and fill each muffin cup about half full with the batter. Then add half a teaspoon of the cinnamon swirl into the center of each muffin and swirl lightly with a toothpick or the end of a small spoon. Take care not to push the cinnamon mixture toward the bottom of the muffin.
4. Bake the muffins: Divide the remaining batter overtop, then add more cinnamon swirl and swirl it in. Bake at 325ºF for 15 to 20 minutes, until the muffins are puffed and golden brown. The very top may not seemed cooked through because of the buttery cinnamon mixture, but it will set when they cool.
5. Make the drizzle: While the muffins cool, whisk together the sweetener and heavy whipping cream in a small bowl. Add water in tiny amounts until a drizzling consistency is achieved. Drizzle over the cooled muffins.
Tips for Success

One of the most important things when making these protein muffins is that you don’t push the cinnamon mixture toward the bottom of the muffin. I did that with a few of them and it’s so buttery that the bottoms come off the muffins as you try to get them out of the liners.
I tried this recipe with both almond flour and coconut flour, and I found that the coconut flour made it very rubbery and eggy. So I can’t recommend it.
Whey protein powder works best here but egg white protein may work as well. Plant protein will likely have too strong a flavor, and collagen will make them gummy.
Sweetener Options
For the filling, you will want a brown sugar replacement. But if you can add a tablespoon of allulose or xylitol as well, it helps make it gooier. If not, it will still be delicious!
The muffin batter can be made with your favorite sweetener. I deliberately didn’t sweeten it as much because the filling adds so much sweetness.
The drizzle requires a powdered sweetener to work properly.

Frequently Asked Questions
This funny curdy cheese is a healthy addition to your low carb diet. Each ½ cup serving of cottage cheese has 12 to 14 grams of protein and only 3 to 5 grams of carbohydrate. I really like the Good Culture brand, for the probiotics as well.
Store these muffins on the counter in a covered container for up to 4 days or in the fridge for up to a week. You can also freeze them for several months.
These keto protein muffins have 4.4g of carbs and 1.7g of fiber per serving. That comes to 2.7g net carbs per muffin.


Cinnamon Protein Muffins Recipe
Ingredients
Cinnamon Swirl
- 1/4 cup (56.75 g) butter, softened, almost melted
- 1/4 cup (50 g) brown sugar replacement
- 1 tbsp allulose, or xylitol
- 1 tbsp ground cinnamon
Muffins
- 3/4 cup (157.5 g) cottage cheese
- 3 large eggs
- 1/3 cup (60.67 g) Swerve Sweetener, (or other granular sweetener)
- 1 tsp vanilla extract
- 1 3/4 cup (196 g) almond flour
- 3/4 cup (81 g) unflavored whey protein powder
- 2 tsp baking powder
- 1/4 tsp salt
Drizzle (optional)
- 1/3 cup (41.67 g) Swerve Confectioners
- 1 tbsp heavy whipping cream
- Water as needed
Instructions
Cinnamon Swirl
- In a medium bowl, stir together the butter, sweeteners, and cinnamon. The butter should be almost melted but not quite, and the mixture should be like a thin paste. Set aside.
Muffins
- Preheat the oven to 325ºF and line the wells of two muffin pans with silicone or parchment liners. If you only have one pan, you may need to work in batches.
- In a blender, combine the cottage cheese, eggs, sweetener, and vanilla, and blend until smooth. Add the almond flour, whey protein, baking powder, and salt and blend again until smooth.
- Fill each muffin cup about half full with the batter. Then add half a teaspoon of the cinnamon swirl into the center of each muffin and swirl lightly with a toothpick or the end of a small spoon. Take care not to push the cinnamon mixture toward the bottom of the muffin.
- Divide the remaining batter overtop, then add more cinnamon swirl and swirl it in.
- Bake 15 to 20 minutes, until the muffins are puffed and golden brown. The very top may not seemed cooked through because of the buttery cinnamon mixture, but it will set when they cool.
- Remove and let cool 20 minutes, then transfer to a wire rack to cool completely.
Optional Drizzle
- In a small bowl, whisk together the sweetener and heavy whipping cream. Add water in tiny amounts until a drizzling consistency is achieved. Drizzle over the cooled muffins.
Notes
Nutrition
Nutritional Disclaimer
Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.
Free Bonus: Secrets to Keto Baking!
Sign up for your favorite recipes delivered straight to your inbox plus get our FREE bonus: Secrets to Keto Baking!






We love these! Even shared the recipe with the lady in our local market. Took her one over and she’s hooked like we are! Super easy, tasty and now my house smells like cinnamon
I always find it a bit irritating when recipes make 14 muffins when muffin tins have only 12 muffin indentions. So, what are we supposed to do with the other 2 muffin ingredients? Waste electricity using an oven for 2 muffins? Throw it away?
Or… get a second muffin pan that holds 6. OR get some of the stiff silicone muffin cups that stand up on their own and put them on a small baking tray along with the others. Really, there are a lot more options than you think – think outside the box.
These look so good! I use pea protein powder & wonder if that is an OK sub for whey protein? Thanks
Going to try these😀
How do you think this would work as a bread instead? I’m too lazy to work in batches. lol
Sorry, I really can’t say for sure. You are welcome to experiment!
I’d really like to try this recipe, but I don’t have a blender that can handle it. Has anyone used a food processor instead? Can anyone think of a reason why this wouldn’t work?
These are great! I followed the recipe except cut down the brown sugar sweetener in the swirl to a TBSP (as I usually do) but did add the TBSP allulose.
I thought the batter was a little dry (used a slightly different whey protein powder) so added about 1/3 cup water). Delicious! Family voted 5 stars!
hi this looks delicious! but we don’t have cottage cheese in india, any good substitute?
Ricotta cheese might work.
This may be real late, but I live in Malaysia. I have had success substituting tofu in certain baked goods. I will try that in these.
Made these today! Perfection!
These are a bit more work than Caroline’s other protein muffin recipes but worth it if you love cinnamon! I’ve made several batches, they turn out perfectly and are delicious.
I made pumpkin protein waffles last weekend and wanted the same flavour but in a muffin. So I made this recipe but put in 1/2 c of pumpkin and 1 tbsp of pumpkin pie spice instead of the cinnamon swirl. (Also I didn’t swirl it, I just blended them with the other ingredients.) They tasted like I wanted but a little dry so I will keep tweaking!
hello! I have a ton of pea protein, as I don’t like the flavor of whey protein. is that an acceptable substitution? I’m new to this Keto baking. thank you!
I use Ritual protein powder, vanilla 8in baking and it works great. You can take out some or all vanilla if you like, add a bit of water to replace, or a bit more plant milk, I use Soy, and it works. I don’t use Allulose, it is not a natural option it is a chemical compound as is Xylitol and erythritol. Monk sugar and stevia are the natural options. The EU is still testing all three for health concerns.
Glad the recipe worked out for you.
You may want to dig into that a bit more, as your comments about sweeteners are incorrect. Allulose, xylitol, and erythritol are NOT chemical compounds, they are all naturally occurring substances. And the EU has approved BOTH erythritol and xylitol, a simple google search will show you that. Allulose has yet to be approved for sale but contrary in the EU, but that doesn’t mean there are health concerns associated with it.
Instead of Whey Protein how about using unflavored beef protein powder? Will that be okay?
No, it won’t. It’s a lot like collagen and makes baked goods very gummy.
I have learned over the years of following (and loving!) your recipes that if you stray from your recommended ingredients…well…you get what you get. Trust in Carolyn!!
I do have a question about the swirl ingredients though and I’ll preface it by the swerve recipe change and adapting makes my head spin a little.
You mention that the new swerve brown isn’t the same because it now contains allulose but your recipe calls for adding allulose to your brown sugar substitute. Would the swerve brown not work here? Again…I trust you…I just am trying to understand the sweetener madness. Lol
Nope… because they only added a little allulose so it changes the recipe but doesn’t help it stay soft enough for the swirl.
I saw your post today with these on face-book and had to make them! While I didn’t measure per muffin cup very well, I managed to even it out and they turned out fantastic! My oven is a bit odd though, I did need to bake them just a bit longer. They just came out of the oven, and I had to taste one right away! Delicious Carolyn! Thanks so much, your recipes always turn out well and taste so good. I can actually eat your baked goods and enjoy them. Many times the flavor and texture just isn’t there when I’ve made other’s recipes.
So glad you like them!
Can allulose be replaced by anything? It’s not sold in my country, so would have to buy it online and wait for it to be delivered.
Please read the Sweetener Options in the Tips section.
The picture with that gooey cinnamon mixture sure looks like it would welcome some finely chopped pecans. I will try that & let you know how it is.