Indulging in a delightful muffin doesn’t have to mean sacrificing your health goals. These Healthy Double Chocolate Chip Muffins with Cream Cheese Filling are a perfect example of how you can enjoy a rich chocolate treat while still keeping things nutritious. With a base of whole wheat flour and a creamy center made with reduced-fat cream cheese, these muffins are both satisfying and guilt-free. Let’s dive into the details of this delicious recipe!
What Sets This Recipe Apart

What makes these Healthy Double Chocolate Chip Muffins truly special is their unique combination of flavors and textures. The use of whole wheat flour and unsweetened cocoa powder creates a hearty base, while the Greek yogurt adds moisture and a protein boost. The cream cheese filling offers a luscious surprise that elevates each bite, making them feel indulgent without the extra calories. Plus, with just a touch of Truvia sweetener and natural honey, you can enjoy a sweet treat without the sugar overload.
What You’ll Gather
- 1 cup (126g) whole wheat flour – This provides a nutty flavor and added fiber.
- 1/2 cup unsweetened cocoa powder – The star ingredient for that rich chocolate flavor.
- 1 teaspoon baking powder – Helps the muffins rise beautifully.
- 1 teaspoon baking soda – Works with the acidic components for an airy texture.
- 1/4 teaspoon sea salt – Enhances the flavors of the other ingredients.
- 1/4 cup Truvia sweetener – A low-calorie sweetener for a guilt-free treat.
- 10 tablespoons vanilla Greek yogurt – Adds creaminess and protein.
- 1/2 cup natural honey – Provides natural sweetness and moisture.
- 1 egg – Binds the ingredients together.
- 1 teaspoon vanilla extract – For that classic cozy flavor.
- 6 tablespoons unsweetened almond milk – Keeps the batter moist.
- 1/2 cup mini chocolate chips – A pop of sweetness in every muffin.
- 6 tablespoons reduced-fat cream cheese – The creamy filling that takes these muffins up a notch.
- 2 tablespoons Truvia sweetener – Sweetens the cream cheese filling.
Equipment Breakdown
- Muffin tin – Essential for shaping your muffins.
- Mixing bowls – For combining ingredients.
- Whisk – To blend dry and wet ingredients smoothly.
- Spoon or spatula – For filling the muffin tin.
- Measuring cups and spoons – For accurate ingredient measurements.
- Cooling rack – Allows muffins to cool evenly.
Mastering Healthy Double Chocolate Chip Muffins with Cream Cheese Filling: How-To

Step 1: Preheat Your Oven
Start by preheating your oven to 350°F (175°C). This ensures that your muffins bake evenly and rise perfectly.
Step 2: Prepare the Muffin Tin
Grease a muffin tin with cooking spray or line it with muffin liners. This will make it easier to remove the muffins later.
Step 3: Combine Dry Ingredients
In a large mixing bowl, whisk together the whole wheat flour, unsweetened cocoa powder, baking powder, baking soda, and sea salt. This ensures the dry ingredients are evenly distributed and ready for mixing.
Step 4: Mix Wet Ingredients
In another bowl, combine the Truvia sweetener, Greek yogurt, honey, egg, vanilla extract, and almond milk. Whisk until smooth and well combined.
Step 5: Combine Wet and Dry Ingredients
Pour the wet mixture into the dry ingredients. Gently fold them together until just combined. Be careful not to overmix, as this can lead to dense muffins.
Step 6: Add Chocolate Chips
Fold in the mini chocolate chips, reserving a few for topping the muffins before baking.
Step 7: Prepare the Cream Cheese Filling
In a small bowl, mix the softened cream cheese with the Truvia sweetener until smooth and creamy. This will be the delicious filling for your muffins.
Step 8: Assemble the Muffins
Spoon a tablespoon of the muffin batter into each muffin cup, followed by a dollop of the cream cheese filling, and then top with more muffin batter to cover the filling. Sprinkle additional chocolate chips on top for an extra touch of sweetness.
Step 9: Bake and Cool
Bake in your preheated oven for 18-20 minutes or until a toothpick inserted into the center comes out clean. Allow the muffins to cool in the tin for a few minutes before transferring them to a cooling rack.
Variations by Season

- Fall: Add in some pumpkin puree and pumpkin spice for a seasonal twist.
- Winter: Incorporate peppermint extract and crushed candy canes for a festive flavor.
- Spring: Mix in fresh berries such as raspberries or blueberries for a fruity surprise.
- Summer: Swap out chocolate chips for dark chocolate chunks or nuts for a different texture.
Watch Outs & How to Fix
Here are a few common issues you might encounter while baking and how to solve them:
- Muffins are too dense: Make sure not to overmix the batter, as this can lead to dense muffins.
- Uneven baking: Ensure your oven is properly calibrated and rotate the muffin tin halfway through baking for even results.
- Filling leaks out: Make sure the cream cheese filling is fully covered by batter before baking.
- Muffins are too sweet: Adjust the amount of Truvia sweetener or honey to suit your taste preferences.
Keep-It-Fresh Plan
These Healthy Double Chocolate Chip Muffins with Cream Cheese Filling can be enjoyed fresh from the oven or stored for later. Here’s how to keep them fresh:
- Room Temperature: Store in an airtight container for up to 3 days.
- Refrigerator: Keep in the fridge for up to a week.
- Freezer: Freeze muffins in a zip-top bag for up to 3 months. Thaw in the fridge or microwave before enjoying.
FAQ
Can I substitute the whole wheat flour with all-purpose flour?
Yes, you can use all-purpose flour, but the muffins will be less hearty and have a different nutritional profile. Whole wheat flour adds fiber and nutrients.
Can I use a different sweetener instead of Truvia?
Absolutely! You can use coconut sugar, maple syrup, or any other sweetener of your choice, but be mindful of the quantity as it may alter the texture.
How can I make these muffins gluten-free?
To make gluten-free muffins, substitute the whole wheat flour with a gluten-free flour blend that measures 1:1.
Can I make these muffins vegan?
Yes! You can replace the egg with a flax egg (1 tablespoon ground flaxseed mixed with 2.5 tablespoons water) and use a plant-based yogurt alternative.
More from the Kitchen
- Healthy Chocolate Muffins
- Banana Chocolate Chip Muffins
- Simple Vegan Chocolate Cake
- Greek Yogurt Muffins
The Takeaway
These Healthy Double Chocolate Chip Muffins with Cream Cheese Filling are the perfect blend of indulgence and nutrition. They showcase how you can enjoy delicious flavors without the guilt. Whether for breakfast, a snack, or a dessert, these muffins satisfy your chocolate cravings while offering wholesome ingredients. Enjoy baking, and don’t forget to share these treats with family and friends—they’ll be impressed by your healthy baking skills!

Healthy Double Chocolate Chip Muffins with Cream Cheese Filling
Equipment
- Muffin Tin
- Mixing Bowls
- Whisk
- Spoon or spatula
- Measuring cups and spoons
- Cooling rack
Ingredients
For the Muffins
- 1 cup whole wheat flour
- 1/2 cup unsweetened cocoa powder
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1/4 teaspoon sea salt
- 1/4 cup Truvia sweetener
- 10 tablespoons vanilla Greek yogurt
- 1/2 cup natural honey
- 1 egg
- 1 teaspoon vanilla extract
- 6 tablespoons unsweetened almond milk
- 1/2 cup mini chocolate chips
For the Cream Cheese Filling
- 6 tablespoons reduced-fat cream cheese softened
- 2 tablespoons Truvia sweetener
Instructions
Preparation
- Preheat your oven to 350°F (175°C) to ensure even baking and perfect rise.
- Grease a muffin tin with cooking spray or line it with muffin liners for easy removal.
Mixing the Batter
- In a large mixing bowl, whisk together whole wheat flour, unsweetened cocoa powder, baking powder, baking soda, and sea salt until evenly combined.
- In another bowl, combine Truvia sweetener, Greek yogurt, honey, egg, vanilla extract, and unsweetened almond milk. Whisk until smooth and well combined.
- Pour the wet ingredients into the dry ingredients and gently fold together until just combined. Avoid overmixing to keep muffins light.
- Fold in mini chocolate chips, reserving a few to sprinkle on top before baking.
Preparing the Filling and Assembling
- In a small bowl, mix softened reduced-fat cream cheese with Truvia sweetener until smooth and creamy for the filling.
- Spoon about a tablespoon of muffin batter into each muffin cup, add a dollop of cream cheese filling, then cover with more batter. Top with remaining chocolate chips.
Baking and Cooling
- Bake muffins in the preheated oven for 18-20 minutes until a toothpick inserted in the center comes out clean.
- Let muffins cool in the tin for a few minutes before transferring to a cooling rack to cool completely.
Notes
- Do not overmix the batter to avoid dense muffins.
- Rotate the muffin tin halfway through baking for even cooking.
- Ensure cream cheese filling is fully covered by batter to prevent leaking.
- Store muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to a week.
- Freeze muffins for up to 3 months and thaw before serving.
