These Healthy Pumpkin Cheesecake Muffins are high in protein and low in calories, making them the ultimate cozy treat. Made with real pumpkin purée, warm spices, and creamy Greek yogurt instead of oil, they’re moist, fluffy, and packed with fall flavor. Each muffin has around 10g of protein and a rich cheesecake center that melts in your mouth. The best part? They taste just like a pumpkin cream cheese muffin from Starbucks– but in a healthy, high-protein form you can enjoy anytime!
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Why You’ll Love These Pumpkin Cheesecake Muffins
While most pumpkin muffins are packed with sugar and oil, my Pumpkin Cheesecake Muffins are a high-protein, low-calorie twist on the classic fall favorite. Made with real pumpkin purée, Greek yogurt, and a touch of protein powder, they’re moist, fluffy, and full of pumpkin spice – without the excess calories. And the best part? The creamy cheesecake center makes them taste indulgent while still being balanced and nourishing.
Each muffin packs 10g of protein and 150 calories, keeping you satisfied and energized throughout the day. They’re naturally sweetened, incredibly easy to make, and ready in under 30 minutes.
They are also a healthier dupe for the Starbucks Pumpkin Cream Cheese Muffin. So if you love Starbucks’ Pumpkin Cream Cheese Muffins but wish they were a little lighter (and packed with protein), these homemade Pumpkin Cheesecake Muffins are exactly what you need.
Macros for Healthy Pumpkin Cheesecake Muffins
Per Muffin (8):
Calories: 150
Carbohydrates: 18g
Protein: 10g
Fat: 4g
Other Protein Muffins to Try
Ingredients and Substitutions for Healthy Pumpkin Cheesecake Muffins
Muffins
Flour- All purpose, can sub for oat flour or gluten free flour
Protein Powder- I use the Vanilla Buttercream Protein from MacroMike. My affiliate code for Macromike is AMB-ELIYEATS (saves you 10%!). Can use whey or any other flavours
Baking Powder
Baking Soda- using both baking powder and soda ensures the muffins rise well and maintains fluffiness
Zero Calorie Granulated Sweetener– I use a zero calorie natural sweetener from Natvia, sub for normal granulated brown or white sugar
Greek Yogurt/Protein Yogurt- I use YoPRO Vanilla Protein Yogurt, plain yogurt will work
Cinnamon or Pumpkin Spice
Vanilla- for flavour
Egg- can sub for a flax egg or extra 70g yogurt
Milk + 1/4 lemon juiced- I use a high protein, low fat milk but you can use a plant milk. Adding the lemon juice will turn the milk into “buttermilk” due to the added acidity. This helps with the fluffiness and overall texture of the muffin
Pumpkin Puree- If you can’t find pumpkin puree you can make your own at home or use baby food
Cream cheese filling
Light Cream Cheese- can sub for normal cream cheese
Icing Sugar- monkfruit icing sugar to keep it sugar free and lower in calories, or normal icing sugar
Vanilla- for flavour
Baking Powder
Baking Tips
Room Temperature Ingredients: Allow ingredients like eggs, milk, and Greek yogurt to come to room temperature before using. This helps them combine more evenly and produces a smoother, fluffier muffin.
Gentle Mixing: When folding wet and dry ingredients together, mix just until combined. Overmixing can make muffins dense or tough, so keep it light for a tender, airy crumb.
Chill the Batter (Optional): Letting the batter rest in the fridge for 30 minutes to an hour (or even overnight) allows the flour to fully absorb the moisture, giving you a thicker, more stable batter. This can help the muffins rise evenly and hold their shape.
Don’t Overfill Muffin Cups: Fill each muffin liner about ¾ full to allow room for rising without spilling over.
Bake at 220c for the first 5 minutes: Baking muffins at a higher temperature initially before lowering the temperature can result in better muffins with a desirable texture and appearance
Check for Doneness: Because ovens vary, start checking your muffins around 20–25 minutes. A toothpick inserted in the center should come out clean (or with just a few moist crumbs).
Cool Before Serving: Let muffins cool in the tin for 5–10 minutes before transferring to a wire rack. This prevents the cheesecake center from sinking and helps them firm up.
How to store Healthy Pumpkin Cheesecake Muffins
Fridge: Place the cooled muffins in an airtight container and store for 3-5 days.
Freezer: If you want to store muffins for an extended period (up to 3 months), freezing is a great option. Wrap each muffin individually in plastic wrap or aluminum foil, then place them in an airtight freezer-safe bag. Thaw frozen muffins at room temperature or gently reheat them in the oven or microwave.
Healthy Pumpkin Cheesecake Muffins (Easy + High Protein Fall Treat)
Ingredients
Method
- In a mixing bowl, combine the egg, pumpkin puree, yogurt, granulated sweetener, cinnamon, vanilla extract and milk. Mix until the ingredients are well combined and the mixture has a creamy texture.
- Sift in the flour, protein powder, baking powder, baking soda, and a dash of salt. Fold the mixture until just incorporated.
- OPTIONAL: Rest and Develop Flavor and texture: For optimal flavor development and texture, cover the muffin batter and refrigerate for a minimum of 30 minutes. This step, while optional, allows the ingredients to harmonize and enhances the taste profile of the muffins.
- Mix the cream cheese mixture until smooth and no clumps remain.
- Preheat your oven to 220°C (428°F). While the oven heats up, prepare 8 muffin liners in a muffin tin.
- Distribute the muffin batter evenly among the prepared liners, making sure to scoop the cheesecake layer in the middle and swirl on top. For optimal results add 8 muffins liners to 2x 6 muffin tin trays, filling up the ones without liners with water. (4 muffins per tray).
- Bake the muffins at 220c for approximately 5 minutes, then drop the temperature to 180c and bake for a further 20-25 minutes or until a toothpick inserted into the center emerges clean.
- Once baked, allow the muffins to cool in the tin for 10-15 minutes, then transfer the muffins to a wire rack for further cooling.
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