These keto cinnamon roll stuffed muffins are one of my favorite low carb breakfast treats. They’re soft, cinnamony, and have a cream cheese filling hiding inside that makes every bite so good.
If you miss cinnamon rolls on a keto diet, this is the recipe for you. You get all those warm, sweet flavors without the carbs and sugar that come with traditional ones.

The batter comes together really quickly using almond flour and a few simple ingredients you probably already have. Nothing complicated here.
Each muffin has a beautiful cinnamon swirl on top and a cream cheese glaze drizzled over it. They look just as good as they taste.
Whether you make them for weekend breakfast or as a snack to have ready during the week, these muffins are a solid choice for anyone eating low carb or keto.
Why You’ll Love This Recipe
Tastes Like a Real Cinnamon Roll – That warm cinnamon swirl with cream cheese filling gives you true cinnamon roll flavor without any of the carbs.

Perfectly Soft and Moist – The sour cream and butter in the batter keep these muffins incredibly tender and never dry or crumbly.
Looks Like a Bakery Treat – The golden tops with cinnamon swirls and drizzled glaze make these look way too fancy for something this easy to make.
Recipe Ingredients
For the Cream Cheese Filling
- 4 oz Cream Cheese, softened
- 1 tbsp Powdered Erythritol
- 1/2 tsp Vanilla Extract
For the Muffin Batter
- 2 cups Almond Flour
- 1/3 cup Granulated Erythritol
- 1 1/2 tsp Baking Powder
- 1/4 tsp Salt
- 3 Large Eggs
- 1/4 cup Melted Butter
- 1/4 cup Sour Cream
- 1 tsp Vanilla Extract
For the Cinnamon Swirl
- 2 tbsp Melted Butter
- 2 tbsp Brown Erythritol
- 1 1/2 tsp Ground Cinnamon
For the Glaze
- 2 oz Cream Cheese, softened
- 2 tbsp Powdered Erythritol
- 2 tbsp Heavy Cream
- 1/2 tsp Vanilla Extract
How To Make
Step 1
Preheat your oven to 350F and line a 12-cup muffin tin with parchment liners. In a small bowl, beat the cream cheese filling ingredients together until smooth, then scoop 12 small balls using a teaspoon and place them on a parchment-lined plate. Freeze for 15 minutes while you prepare everything else.
Step 2
In a large bowl, whisk together the almond flour, granulated erythritol, baking powder, and salt.
Step 3
Add the eggs, melted butter, sour cream, and vanilla extract to the dry ingredients. Stir until a thick, smooth batter forms with no lumps.
Step 4
In a small bowl, stir together the melted butter, brown erythritol, and cinnamon for the swirl until well combined.
Step 5
Spoon about 1 tablespoon of muffin batter into each liner. Place one frozen cream cheese ball on top of the batter in each cup, then divide the remaining batter evenly over the cream cheese balls.
Step 6
Drizzle the cinnamon swirl mixture over the top of each muffin. Use a toothpick to gently swirl it into the batter in a figure-eight motion, keeping most of the swirl visible on top.
Step 7
Bake for 22 to 25 minutes, until the tops are golden and a toothpick inserted near the edge comes out clean. Let the muffins cool in the tin for 10 minutes, then transfer to a wire rack.
Step 8
While the muffins cool, whisk together the glaze ingredients until completely smooth. Drizzle generously over the warm muffins and serve.

Tips
Freeze the Cream Cheese Balls Properly
Don’t skip the freezing step or cut it short. If the cream cheese balls are still soft when you put them in the batter, they’ll melt into the muffin and you won’t get that distinct creamy pocket in the center.
15 minutes is the minimum. If they still feel squishy when you touch them, give them another 5 minutes. You want them firm enough to hold their shape while you press batter around them.
A quick trick is to use a small cookie scoop or teaspoon to make them roughly the same size. That way every muffin gets an even amount of filling.
Use Parchment Liners Instead of Regular Ones
Almond flour batter sticks to regular paper cupcake liners really badly. You’ll peel the liner off and half the muffin will come with it. Parchment liners release much more cleanly.

If you can’t find parchment liners, you can also grease regular silicone liners with a little butter or cooking spray. But parchment is the easiest and most reliable option for these.
Get the Cinnamon Swirl Right
When you drizzle the cinnamon mixture on top, don’t dump it all in one spot. Use a small spoon and drizzle it in thin lines across the surface of each muffin so it’s easier to swirl.
When you use the toothpick, do a gentle figure-eight motion and only go about halfway down into the batter. If you push too deep, you’ll disturb the cream cheese ball sitting in the middle.
You want most of the swirl to stay visible on top. That’s what gives these muffins that classic cinnamon roll look after baking.
More Recipes
- Keto Cinnamon Roll Cheesecake
- Keto Cinnamon Roll Mug Cake
- Keto Blueberry Muffins
- Low Carb Glazed Cinnamon Rolls
- Keto Cinnamon Swirl Coffee Cake
Frequently Asked Questions
Can I use coconut flour instead of almond flour for these muffins?
Coconut flour is not a simple 1:1 swap here. It absorbs way more liquid than almond flour, so you would need roughly 1/3 of the amount and probably an extra egg or two to keep the batter from being too dry and crumbly.
If you do try it, start with about 1/3 cup of coconut flour and add an extra egg. The texture will be slightly different, but it can still work in a pinch if almond flour is not an option for you.
Keto Cinnamon Roll Stuffed Muffins
Ingredients
Equipment
Method
- Preheat your oven to 350F and line a 12-cup muffin tin with parchment liners. In a small bowl, beat the cream cheese filling ingredients together until smooth, then scoop 12 small balls using a teaspoon and place them on a parchment-lined plate. Freeze for 15 minutes while you prepare everything else.
- In a large bowl, whisk together the almond flour, granulated erythritol, baking powder, and salt.
- Add the eggs, melted butter, sour cream, and vanilla extract to the dry ingredients. Stir until a thick, smooth batter forms with no lumps.
- In a small bowl, stir together the melted butter, brown erythritol, and cinnamon for the swirl until well combined.
- Spoon about 1 tablespoon of muffin batter into each liner. Place one frozen cream cheese ball on top of the batter in each cup, then divide the remaining batter evenly over the cream cheese balls.
- Drizzle the cinnamon swirl mixture over the top of each muffin. Use a toothpick to gently swirl it into the batter in a figure-eight motion, keeping most of the swirl visible on top.
- Bake for 22 to 25 minutes, until the tops are golden and a toothpick inserted near the edge comes out clean. Let the muffins cool in the tin for 10 minutes, then transfer to a wire rack.
- While the muffins cool, whisk together the glaze ingredients until completely smooth. Drizzle generously over the warm muffins and serve.