There’s something magical about the smell of cinnamon rolls baking in the oven on a lazy Sunday morning. However, those traditional pastries aren’t exactly the best choice when you’re trying to fuel your body with quality nutrition. That’s exactly why I created these Cinnamon Roll Protein Muffins—they capture all the cozy, sweet flavors of classic cinnamon rolls while packing in protein to keep you satisfied for hours.
I first made these muffins on a particularly busy Monday morning when I needed something quick, delicious, and energizing. After one bite, I was hooked. The tender crumb, the swirls of cinnamon sugar, and that drizzle of vanilla glaze made me feel like I was indulging in dessert for breakfast. Best of all, I didn’t experience that mid-morning energy crash I usually get from sugary pastries.
Why You’ll Love This Recipe
These protein muffins aren’t just another boring healthy breakfast option. Instead, they’re genuinely delicious treats that happen to be good for you. Each muffin delivers a solid protein boost thanks to the protein powder and Greek yogurt, making them perfect for post-workout snacks or busy mornings when you need sustained energy.
What makes these particularly special is their incredible texture. Unlike many protein-based baked goods that turn out dry and crumbly, these muffins are wonderfully moist and tender. The combination of almond flour and coconut flour creates a delicate crumb that rivals any bakery muffin.
Perfect for Meal Prep
Another reason I keep coming back to this recipe is how well these muffins store. You can bake a batch on Sunday and have grab-and-go breakfasts ready for the entire week. They freeze beautifully too, which means you can always have a healthy treat on hand when cravings strike.
The cinnamon swirl isn’t just for show—it creates pockets of sweet, spiced flavor throughout each muffin. Meanwhile, the optional vanilla glaze adds that authentic cinnamon roll experience without loading up on refined sugar.
Ingredients
Main Muffin Components
- 1 cup vanilla protein powder
- 1 cup almond flour
- 1/4 cup coconut flour
- 1/4 cup Greek yogurt
- 1/4 cup almond milk
- 2 eggs
- 2 tbsp melted coconut oil
- 1/4 cup maple syrup
- 1 tsp vanilla extract
- 1 ½ tsp cinnamon
- 1/2 tsp baking soda
- 1/4 tsp salt
Cinnamon Swirl
- 2 tbsp coconut sugar
- 1 tsp cinnamon
Vanilla Glaze (Optional but Recommended)
- 2 tbsp powdered monk fruit sweetener
- 1-2 tsp almond milk
- 1/4 tsp vanilla extract
Step-by-Step Instructions
Preparing Your Kitchen
Start by preheating your oven to 350°F (175°C). While the oven heats up, line a muffin tin with 10 paper liners. This recipe makes exactly 10 muffins, so you’ll have one standard muffin pan filled plus two extra spots for bonus treats.
Mixing the Dry Ingredients
Grab a large mixing bowl and whisk together your protein powder, almond flour, and coconut flour. Add the cinnamon, baking soda, and salt to this mixture. Whisking thoroughly at this stage ensures that the leavening agents and spices distribute evenly throughout your muffins, which prevents any baking soda clumps or flavor inconsistencies.
Combining the Wet Ingredients
In a separate bowl, crack and beat your eggs until they’re well combined. Then, stir in the Greek yogurt, making sure it’s fully incorporated with the eggs. Next, add your maple syrup, almond milk, melted coconut oil, and vanilla extract. Mix everything together until you have a smooth, uniform wet mixture.
Creating the Batter
Pour your wet ingredients into the bowl with the dry ingredients. Using a spatula or wooden spoon, gently fold everything together until you achieve a smooth batter. Be careful not to overmix—stirring just until the ingredients are combined will give you the most tender muffins.
Making the Cinnamon Swirl
While your batter rests for a moment, prepare your cinnamon swirl by mixing the coconut sugar and cinnamon in a small bowl. This simple mixture is what transforms ordinary muffins into cinnamon roll-inspired delights.
Assembling the Muffins
Here’s where the fun begins. Fill each muffin liner about halfway with batter—this creates the base layer. Sprinkle a generous amount of your cinnamon swirl mixture over this first layer. Then, top off each muffin cup with the remaining batter, dividing it evenly among all 10 liners.
Creating the Swirl Effect
Take a toothpick and insert it into each muffin, swirling it in a circular motion to create that signature cinnamon roll pattern. Don’t worry about making it perfect—the swirls will look beautiful no matter what, and some variation actually makes them look more artisanal and homemade.
Baking to Perfection
Place your muffin tin in the preheated oven and bake for 20–22 minutes. You’ll know they’re done when a toothpick inserted into the center comes out clean. The tops should be golden and slightly springy to the touch.
Cooling and Glazing
Remove the muffins from the oven and let them cool in the pan for about 5 minutes. Then, transfer them to a wire rack to cool completely. This cooling step is crucial—adding the glaze to warm muffins will cause it to melt and run off.
While the muffins cool, whisk together your powdered monk fruit sweetener, almond milk, and vanilla extract until smooth. Once the muffins have reached room temperature, drizzle this vanilla glaze over the tops using a spoon or a small piping bag.

Serving Suggestions
These muffins are incredibly versatile and can be enjoyed in numerous ways. For a classic breakfast, pair one or two muffins with a hot cup of coffee or tea. The protein content makes them substantial enough to keep you full until lunch, especially if you add a piece of fruit on the side.
If you’re looking for a post-workout snack, these muffins are ideal. The protein helps with muscle recovery, while the natural sugars from the maple syrup provide quick energy. Try warming one up in the microwave for about 15 seconds—it makes the muffin taste fresh from the oven.
Creative Serving Ideas
For a more indulgent breakfast or brunch, slice a muffin in half and spread a thin layer of almond butter or cashew butter on each side. The nut butter adds healthy fats and makes the treat even more satisfying. You could also crumble a muffin over Greek yogurt with fresh berries for a protein-packed parfait.
Kids absolutely love these muffins as after-school snacks. Pack one in their lunchbox as a healthier alternative to store-bought treats. The familiar cinnamon roll flavor makes them more appealing than typical “healthy” options.
Recipe Variations
Chocolate Lovers’ Version
Want to switch things up? Try adding 2 tablespoons of cocoa powder to the dry ingredients and folding in 1/4 cup of dark chocolate chips. This creates a chocolate-cinnamon combination that tastes like a Mexican hot chocolate in muffin form.
Nutty Delight
For extra texture and flavor, fold in 1/3 cup of chopped pecans or walnuts into the batter before filling the muffin cups. Alternatively, sprinkle chopped nuts on top of the muffins before baking for a crunchy topping.
Apple Cinnamon Twist
Dice half an apple into small pieces and fold them into the batter along with an extra 1/4 teaspoon of cinnamon. This variation adds natural sweetness and moisture while giving you a taste of fall in every bite.
Pumpkin Spice Version
During autumn months, replace 2 tablespoons of the Greek yogurt with pumpkin puree and add 1/4 teaspoon each of nutmeg and ginger to the dry ingredients. You’ll have pumpkin spice protein muffins that rival any coffee shop treat.
Make-Ahead Tips
These muffins are meal prep champions. Once completely cooled, store them in an airtight container at room temperature for up to 3 days. If you want to extend their freshness, keep them in the refrigerator for up to a week.
Freezing Instructions
For longer storage, these muffins freeze exceptionally well. Place cooled muffins (without glaze) in a freezer-safe bag or container, separating layers with parchment paper. They’ll stay fresh in the freezer for up to 3 months.
When you’re ready to enjoy a frozen muffin, simply remove it from the freezer the night before and let it thaw at room temperature. Alternatively, microwave a frozen muffin for 30-45 seconds for a quick warm treat. Add the vanilla glaze after thawing or reheating for the best presentation.
Glaze Storage
If you’re meal prepping, consider storing the glaze separately in a small container in the refrigerator. This way, you can drizzle fresh glaze on each muffin right before eating, which keeps the muffins from getting soggy and makes them taste freshly made.
Notas
Protein Powder Selection: The type of protein powder you use significantly affects the final texture and flavor. I’ve had the best results with whey or plant-based vanilla protein powders that are lightly sweetened. Avoid using unflavored protein powder, as it can make the muffins taste bland. If your protein powder is very sweet, you might want to reduce the maple syrup slightly.
Flour Substitutions: While I recommend sticking with the almond and coconut flour combination for the best texture, you can experiment with substitutions. Keep in mind that coconut flour is extremely absorbent—if you try replacing it with more almond flour, you’ll need to reduce the liquid ingredients or your batter will be too thin.
Sweetener Options: Maple syrup adds a lovely flavor and moisture to these muffins. However, if you prefer a sugar-free option, you can substitute it with the same amount of sugar-free maple-flavored syrup or honey. Just note that different sweeteners can affect the final texture slightly.
Checking Doneness: Oven temperatures can vary, so start checking your muffins at the 20-minute mark. The toothpick test is reliable, but you can also gently press the top of a muffin—if it springs back, it’s done. Overbaking will result in dry muffins, so it’s better to err on the side of slightly underbaking.
Greek Yogurt Thickness: Use full-fat or 2% Greek yogurt for the best texture. Non-fat Greek yogurt can work, but the muffins may be slightly less moist. Make sure your yogurt is plain and unsweetened—flavored yogurts will alter the taste and add unnecessary sugar.

Frequently Asked Questions
Can I use a different type of milk?
Absolutely! Any milk works well in this recipe. If you’re not dairy-free, regular cow’s milk is perfectly fine. Other plant-based options like oat milk, cashew milk, or coconut milk from a carton (not canned) will also work beautifully. The key is using unsweetened milk to control the sugar content.
How much protein is in each muffin?
Each muffin contains approximately 12-15 grams of protein, depending on the specific brand of protein powder you use. This makes them a substantial snack or breakfast option that will keep you satisfied for hours.
Can I make these muffins without the glaze?
Of course! The muffins are delicious on their own, and skipping the glaze saves you a few minutes and reduces the sugar content. The cinnamon swirl provides plenty of sweetness, so the glaze is truly optional and just adds that authentic cinnamon roll experience.
Why are my muffins dense or rubbery?
This usually happens from overmixing the batter or using too much protein powder. When combining wet and dry ingredients, mix just until everything is incorporated—you should still see a few small lumps. Additionally, make sure you’re measuring your protein powder correctly by spooning it into the measuring cup rather than scooping directly from the container, which can pack it down.
Can I make these as mini muffins?
Yes, this recipe adapts well to mini muffin tins. You’ll get about 24 mini muffins, and you’ll need to reduce the baking time to approximately 12-15 minutes. Keep an eye on them and use the toothpick test to check for doneness.
What’s the best way to reheat these muffins?
For the best texture, microwave individual muffins for 15-20 seconds. This warms them through without drying them out. If you prefer using the oven, wrap muffins in foil and warm at 300°F for about 5-7 minutes. Avoid reheating glazed muffins in the oven, as the glaze may melt off.
Can I double this recipe?
Definitely! This recipe doubles easily if you want to make a larger batch for meal prep or to share. Just make sure you have enough muffin tins, or bake them in batches. The batter can sit at room temperature while the first batch bakes—just give it a quick stir before filling the second batch of liners.
Are these muffins kid-friendly?
Most children love these muffins because they taste like a treat rather than “health food.” The cinnamon roll flavor is familiar and appealing. If you’re making them for young children, you can reduce the cinnamon slightly if they’re sensitive to spices, though most kids enjoy the warm cinnamon flavor.