These Carrot Cake Cheesecake Muffins are high in protein and low in calories, making them a deliciously healthier treat. With no refined sugar and Greek yogurt replacing excess oil, they stay moist, fluffy, and flavorful. Each muffin contains 10g of protein, shredded carrot, and a creamy cheesecake center for the perfect indulgence. The best part? They taste just like classic carrot cake but are a healthier alternative you’ll love!

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Why you will love these Carrot Cake Cheesecake Muffins

While most carrot cake muffins are loaded with sugar and oil, my Carrot Cake Cheesecake Muffins are a high-protein, low-calorie twist on the classic. Made with Greek yogurt and a touch of protein powder, these muffins are moist, fluffy, and bursting with warm cinnamon spice—all without the excess calories. And the best part? The creamy cheesecake center adds an indulgent touch while keeping things balanced and nutritious.

Each muffin packs 10g of protein, making them the perfect snack to keep you satisfied and energized throughout the day. They’re naturally sweetened, incredibly easy to make, and ready in under 30 minutes. No dry, dense, or chalky textures here—just soft, bakery-style muffins that taste just as good as the real thing! Whether you need a protein-packed breakfast, a post-workout snack, or a healthier dessert, these muffins are sure to become a new favorite.

Macros for Carrot Cake Cheesecake Muffins

Per Muffin (8):

Calories: 180

Carbohydrates: 17g

Protein: 10g

Fat: 7g

Ingredients and Substitutions for Carrot Cake 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- Essential for that apple crumble flavour

Vanilla- for flavour

Light Butter- Can substitute with normal butter or vegan butter

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

Carrot

Cream cheese filling

Light Cream Cheese- can sub for normal cream cheese

Milk- to thin slightly

Icing Sugar- monkfruit icing sugar to keep it sugar free and lower in calories, or normal icing sugar

Vanilla- for flavour

Baking Tips

Room Temperature Ingredients: Allow ingredients like eggs and milk to come to room temperature before using them. This promotes even mixing and better incorporation of ingredients.

Gentle Mixing: When combining wet and dry ingredients, avoid overmixing. Overmixing can lead to dense and tough muffins. Mix until the ingredients are just incorporated to maintain a tender crumb.

Let batter sit in the fridge: From 30 minutes to overnight, this helps the flour to absorb more moisture, resulting in a thicker batter. A slightly thicker batter can help muffins maintain their shape and rise more evenly.

Proper Filling: Use an ice cream scoop or a spoon to evenly fill the muffin cups. This ensures consistent muffin sizes and even baking.

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

Cooling Time: Allow your muffins to cool in the pan for about 5-15 minutes after baking. Then, transfer them to a wire rack to cool completely. This prevents them from becoming soggy due to trapped steam.

How to store Carrot Cake 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.

The Best Carrot Cake Cheesecake Muffins (Low-Calorie & High-Protein!)

These Carrot Cake Cheesecake Muffins are high in protein and low in calories, making them a deliciously healthier treat. With no refined sugar and Greek yogurt replacing excess oil, they stay moist, fluffy, and flavorful. Each muffin contains 10g of protein, and features a warm cinnamon flavour, shredded carrot, and a creamy cheesecake center for the perfect indulgence. The best part? They taste just like classic carrot cake but are a healthier alternative you’ll love!

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Prep Time 10

Cook Time 25

Chill Time 30

Course Dessert

Servings 8

Calories 180 kcal

Ingredients

Muffin

50 g light butter melted and cooled slightly
80 g yogurt room temp, vanilla or plain
1 egg room temp
160 ml high protein light milk 2/3 cup/160ml + dash of lemon juice to make buttermilk (can use normal milk or plant-based option)
1 tsp vanilla
70 g granulated sweetener A zero calorie sweetener was used in this recipe (see notes) or you can use normal sugar/brown sugar/monkfruit OR a mix of both sweeteners
140 g flour sub for oat flour for gf option
60 g vanilla protein *see notes, can sub for flour
2-3 tsp cinnamon
1.5 tsp baking powder
1/2 tsp baking soda
1/4 tsp salt
200 g shredded carrot 2-3 carrots

Cream Cheese Filling

80 g light cream cheese sub for full fat
1-2 tsp milk
1 tbsp monkfruit icing sugar sub for normal icing sugar

Instructions

In a mixing bowl, combine the melted light butter, granulated sweetener and vanilla extract. Mix until the ingredients are well combined and the mixture has a creamy texture.
Add the egg, yogurt, and buttermilk (prepared by combining milk with the juice of 1/4 lemon). Mix thoroughly until the wet ingredients are fully integrated.
Sift in the flour, protein powder, baking powder, baking soda, cinnamon and a dash of salt. Then add the shredded carrot and mix and 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. 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.

Notes

*This recipe uses a zero calorie granulated sweetener Natvia that has a 1:1 substitution to white sugar. Please make sure if you are going to use a sugar substitute that it has the same substitution. If the sweetness is more concentrated, please use less of the sweetener.

*Protein used: Vanilla Buttercream from MacroMike. My affiliate code for Macromike is AMB-ELIYEATS (saves you 10%!)- If using whey protein, add less milk!