
These cinnamon roll protein muffins are my go to healthy breakfast treat when I want something sweet that will keep me satisfied all morning. Packed with vanilla and cinnamon flavor plus a touch of maple syrup you would never guess they are so high in protein and lower in sugar than traditional muffins.
I started making these muffins after my kids asked for cinnamon rolls every weekend. Once I found this healthier version with added protein everyone was on board and now we all look forward to them on Saturday mornings.
Ingredients
- Eggs: add structure moisture and extra protein for a fluffy muffin. Choose fresh large eggs for best results
- Plain Greek yogurt: brings moisture tang and most of the protein. Look for a thick strained style
- Unsweetened almond milk: gives a light texture without adding much fat or sugar. Shelf stable is great for convenience
- Unsweetened applesauce: replaces some oil and keeps muffins tender. Use a good quality applesauce with no sugar added
- Maple syrup or honey: provides natural sweetness and a subtle flavor. Go for pure maple syrup if you can
- Vanilla extract: boosts the bakery style flavor. True vanilla extract makes a difference
- Oat flour or finely ground oats: boost fiber and keep things gluten friendly if using certified oats. Grind your own oats for extra freshness
- Vanilla protein powder: gives each muffin a big protein boost. Try a cleaner whey or plant based protein with short ingredients
- Coconut flour: soaks up moisture and increases fiber. Make sure your flour is fresh with no odd odors
- Baking powder and baking soda: help muffins rise tall and stay fluffy. Check expiration dates for best lift
- Salt: balances the sweet notes. Fine sea salt is ideal for even seasoning
- Coconut sugar or brown sugar: gives the cinnamon swirl a deep caramel note. Choose soft moist sugar for better mixing
- Ground cinnamon: delivers that signature swirl. Freshly opened cinnamon makes a world of difference
- Low fat cream cheese: is creamy and adds tang to the optional topping. Ensure it is very soft for easy blending
- Greek yogurt in the topping: makes it lighter and more tangy
- Maple syrup in the topping: keeps the glaze naturally sweet
Step-by-Step Instructions
- Preheat Oven:
- Set your oven to 350 degrees Fahrenheit or 175 degrees Celsius and get your muffin tin ready. Use paper liners or a light mist of oil spray to help muffins release easily
- Mix the Wet Ingredients:
- In a big bowl thoroughly whisk eggs Greek yogurt almond milk applesauce maple syrup and vanilla. Make sure the mixture is smooth and even so your muffins bake up light
- Combine the Dry Ingredients:
- In another bowl blend together oat flour protein powder coconut flour baking powder baking soda and salt. Use a fork or whisk to break up any lumps for an even batter
- Combine Wet and Dry Ingredients:
- Gently fold the dry mixture into the wet mixture just until you see no streaks of flour. Be careful not to overmix or your muffins may turn out dense
- Make the Cinnamon Swirl:
- In a small bowl stir together the coconut or brown sugar and cinnamon until well combined. This mixture will create sweet ribbons in your muffins
- Layer Batter and Swirl:
- Spoon enough batter to fill each muffin cup halfway. Sprinkle a generous pinch of the cinnamon sugar swirl on top then cover with the remaining batter. Use a toothpick to swirl gently without mixing entirely
- Bake the Muffins:
- Bake in the center of the oven for eighteen to twenty two minutes. Muffins are done when golden and a toothpick comes out clean from the center
- Prepare Optional Topping:
- Blending softened cream cheese Greek yogurt and maple syrup makes a creamy glaze. Drizzle over the fully cooled muffins for a real bakery touch

My favorite ingredient in this recipe is the thick tangy Greek yogurt. I love how it makes the crumb soft and adds a rich flavor without a lot of fat. My kids call these “cinnamon roll cupcakes” and beg to help swirl the cinnamon in every batch
Storage Tips
Store leftover muffins in an airtight container in the fridge for up to five days. For longer storage place in the freezer and thaw overnight or microwave for a quick breakfast on busy mornings. The texture stays soft even after chilling if you let them reach room temperature before eating
Ingredient Substitutions
If you do not have oat flour finely ground whole wheat flour works well and adds a nutty flavor. For dairy free use coconut yogurt and plant based protein powder. For a little crunch add chopped walnuts or pecans to the batter or sprinkle on top before baking
Serving Suggestions
These muffins are great warm or at room temperature for breakfast or snack. Serve with a smear of nut butter or a side of fruit. Pair with coffee or tea or enjoy as a kid friendly after school treat

Cultural and Historical Context
Cinnamon rolls are a classic breakfast pastry in American kitchens but this version lightens things up without losing flavor. Protein baked goods have become popular for active families and health focused eaters who still want something sweet
Recipe FAQs
- → How do I keep the muffins moist?
Greek yogurt and applesauce help retain moisture, so avoid overbaking and mix the batter just until combined.
- → Can I use different protein powders?
Both plant-based and whey protein powders work well; choose your favorite for the desired flavor and texture.
- → Is there a dairy-free alternative?
Use plant-based yogurt and a dairy-free protein powder. Swap cream cheese with vegan alternatives for the topping.
- → How do I create the cinnamon swirl effect?
Layer the batter with cinnamon-sugar mixture, then swirl gently with a toothpick before baking for a marbled look.
- → Can I add nuts or other mix-ins?
Chopped walnuts or pecans add texture and flavor. Fold them in with dry ingredients before combining all components.
- → How should the muffins be stored?
Cool fully, then store in an airtight container at room temperature for up to 2 days, or refrigerate for longer freshness.