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Healthy Double Chocolate Chip Muffins with Cream Cheese Filling

vg
5 from 2 votes
Taylor KiserBy Taylor Kiser
Taylor Kiser
Taylor Kiser Founder of Food Faith Fitness

Taylor Kiser is a Certified Personal Trainer and Nutrition Coach and a lover of health and fitness. A follower of Christ. Recipe developer. Photographer. Obsessed with cookie dough, pink & leop…

Expertise: Healthy Food View all posts →
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These whole-wheat Healthy Double Chocolate Chip Muffins are stuffed with cream cheese and are the perfect 150-calorie treat! 

Healthy, Cream-Cheese Filled Chocolate Chip Muffins - Whole wheat and only 150 calories but SO moist and chocolatey! | Foodfaithfitness.com | #muffin #recipe #healthy

These muffins don’t just double up on the chocolate, they double up on the health benefits too! With only 150 calories in each muffin, they’re the perfect breakfast pick-me-up, midday treat, or post-dinner dessert.

And with that cream cheese stuffing, giving both a pop of color and a burst of creamy, fresh flavor, it will be hard to resist going back for a second, or third, or fourth…

No matter how many you have, these muffins also store perfectly in the freezer, so whenever you’re in a rush, just grab, microwave, and go!

Healthy, Cream-Cheese Filled Chocolate Chip Muffins - Whole wheat and only 150 calories but SO moist and chocolatey! | Foodfaithfitness.com | #muffin #recipe #healthy

Are Double Chocolate Chip Muffins Healthy?

Unfortunately, like all sweet desserts, these beautiful stuffed muffins do need to be enjoyed in moderation. However, there are still a few health benefits you’ll receive from delighting in one or two occasionally!

For example, whole wheat flour is a good source of fiber, vitamins, and minerals compared to refined flour. Meanwhile, cocoa powder is rich in antioxidants, which can have heart health benefits, and when unsweetened, it is also very low in sugar. You’ll also get protein from the Greek yogurt, and to sweeten the deal, these muffins swap sugar for zero-calorie sweetener.

Flavor Variations

If the cream cheese and chocolate is too simple for you, don’t fret! There are plenty of upgrades you can make to this recipe to make it suit what you’ve got on hand.

Cinnamon: Add a bit of spice to the muffins with a dash of cinnamon.

Berries: Blueberries or raspberries – fresh or frozen – would add a fruity twist to the muffins, and go perfectly with cream cheese and chocolate.

Nuts: Chopped almonds or pecans can be added to the batter or sprinkled on top for a crunchy texture and nutty flavor.

Swirl: Why stop at cream cheese? Why not swirl in some Nutella or peanut butter to the stuffed filling?

Lemon: Add some lemon zest to the cream cheese for a tangy treat.

How To Make Ahead and Store

Allow the muffins to cool completely before storing them in an airtight container or resealable plastic bag. You can keep them at room temperature for 2 days, or in the refrigerator for up to 5 days. To reheat, just microwave for 15 to 20 seconds or put them in the oven at 350°F for 5 to 7 minutes. For long-term storage, freeze the muffins for up to 3 months, and let them thaw in the refrigerator overnight before reheating.

Serving Suggestions

There are few things in life that are better than oven-fresh muffins with a scoop of ice cream. Seriously! My favorites are this Ice Cream with Chocolate and Pomegranate, or this Coconut Milk Ice Cream with Rum and “Egg nog”, but for a healthier option, these muffins also go great with this Frozen Yogurt. When I’m feeling really fancy, I also like to garnish the muffins with this Vegan Caramel Sauce!

Healthy, Cream-Cheese Filled Chocolate Chip Muffins - Whole wheat and only 150 calories but SO moist and chocolatey! | Foodfaithfitness.com | #muffin #recipe #healthy
Healthy, Cream-Cheese Filled Chocolate Chip Muffins - Whole wheat and only 150 calories but SO moist and chocolatey! | Foodfaithfitness.com | #muffin #recipe #healthy

Recipe

Healthy Double Chocolate Chip Muffins with Cream Cheese Filling

5 from 2 votes
Print Rate
Serves: 12 muffins
Chocolate muffin
Prep: 10 minutes minutes
Cook: 18 minutes minutes
Total: 28 minutes minutes

Ingredients

  • 1 cup (126g) 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 plus more for sprinkling

For the filling:

  • 6 tablespoons reduced-fat cream cheese softened at room temperature
  • 2 tablespoons Truvia sweetener

Instructions

  • Preheat your oven to 350°F and spray a muffin tray with cooking spray.
  • In a medium bowl, stir together the flour, cocoa powder, baking powder, baking soda, salt, and Truvia until well mixed.
  • In a separate, large bowl, whisk together the Greek yogurt, and the honey, egg, vanilla extract, and almond milk.
  • Add the dry ingredients and chocolate chips to the wet ingredients, and stir gently until just combined, being careful not to over-mix.
  • In a small bowl, stir together the softened cream cheese and Truvia until well mixed.
  • Fill each muffin cup only half of the way full, and make a small depression in the center of the batter. Drop 1/2 tablespoon of the cream cheese mixture into the center of each muffin. Cover with a spoonful of the remaining batter and gently spread to cover the cream cheese. Your muffin tray cups should only be about 3/4 of the way full, or else your muffins will be too big and flatten.
    Healthy, Cream-Cheese Filled Chocolate Chip Muffins - Whole wheat and only 150 calories but SO moist and chocolatey! | Foodfaithfitness.com | #muffin #recipe #healthy
  • Bake until a toothpick inserted in the center comes out clean, about 17 to 18 minutes. Be careful not to over-bake these as they go from perfect to dry quickly.
  • Let muffins cool in the muffin tray for 10 minutes and then transfer to a rack to finish cooling.

Nutrition Info:

Calories: 151kcal (8%) Carbohydrates: 31g (10%) Protein: 4g (8%) Fat: 4g (6%) Saturated Fat: 2g (13%) Sodium: 191mg (8%) Fiber: 3g (13%) Sugar: 18g (20%)

Nutrition Disclaimer

Nutrition information are estimates only and may vary based on the specific brands, ingredients, and portion sizes you use. This data is provided for informational purposes only.

Author: Taylor Kiser
Course:Desserts, Snacks
Cuisine:American
Share your creationsTag @foodfaithfit and hashtag it #foodfaithfitness so I can see what you made!
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About Taylor KiserHealthy Food

Taylor Kiser is a Certified Personal Trainer and Nutrition Coach and a lover of health and fitness. A follower of Christ. Recipe developer. Photographer. Obsessed with cookie dough, pink & leopard print.

Reader Interactions

Paola Westbeek

✓Reviewed by Paola WestbeekGastronomy & Fine Wines

Published: Sep 8, 2024 | Updated: Sep 2, 2025
5 from 2 votes (2 ratings without comment)

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