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Home » Breakfast

Double Chocolate Cream Cheese Muffins {Gluten Free, Dairy Free}

Published: Apr 25, 2023 · Modified: Apr 25, 2025 by Katie Adams · This post may contain affiliate links · Leave a Comment

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Gluten Free, Dairy Free, Soy Free

Sweet tooth calling for chocolate? These tender muffins' winning combination of bittersweet chocolate and tangy sweet cream cheese will tame your fiercest chocolate craving! Plus, they are so moist and fluffy, you'll forget you're eating gluten free! What are you waiting for? Let’s start baking!

Double Chocolate Cream Cheese Muffins on a plate next to chocolate chips.

Why I Love This Recipe

This soft, fluffy breakfast treat is lusciously chocolate from both cacao powder and chocolate chips deliciously paired with tangy dairy free cream cheese! Perfect for a quick breakfast, snack, or treat, your family will love this allergy friendly recipe!

Soft, moist Double Chocolate Cream Cheese Muffins are tender and fluffy with gooey bites of chocolate chips balanced by creamy, bright cream cheese! This rich, indulgent treat is easy to make and made extra pillowy from the addition of oat flour.

These gluten-free, dairy-free Double Chocolate Cream Cheese Muffins are tender, moist and decadent! Also, to add some sneaky nutrients into my chocolate recipes, I enjoy using unprocessed cacao powder instead of traditional cocoa powder. Cacao is extra rich and delicious, albeit slightly more bitter, with the added benefit of being calcium and antioxidant packed. You can also use traditional cocoa powder if that's what you have on hand.

Stacked Double Chocolate Cream Cheese Muffins on a plate with a tin of muffins, linen napkin, and chocolate chips in the background.

Dairy free cream cheese

Additionally, I like kitehill  or Miyoko’s brand cream cheese. Dairy free cream cheeses tend to contain more liquid so make sure to drain any excess before using. Be aware, both these brands do contain nuts. Violife makes a nut free, dairy free cream cheese, however I have never used it. I do eat a lot of their dairy free, nut free cheese products and the quality is always very good. 

Cacao vs cocoa powder

Cacao powder is minimally processed and retains more nutrients. It is rich in antioxidants, minerals, and also has a deeper more bitter flavor. Don't have cacao powder on hand? Feel free to substitute with cocoa powder. The taste will be very similar.

Why is vinegar in this recipe?

Moreover, make sure you don't skip the apple cider vinegar in this recipe! It's what activates the baking soda and causes the muffins to rise.

Let's talk xanthan gum

Xanthan gum can be found in the allergy friendly section of most grocery stores’ baking aisle. It's Whole30 and Paleo approved and helps to bind this gluten-free batter together. Xanthan gum allows baked good to hold moistness and structure. Many pre-mixed gluten free flours contain a binder of some sort, usually xanthan or guar gum. You could try leaving it out if you really want to. However, the muffins may be less tender and moist.

Cross section of a Double Chocolate Cream Cheese Muffin with a tin of muffins, plate of muffins, chocolate chips, and cacao powder in the background.

Storage Instructions

Finally, store these muffins at room temperature up to 4 days. Use an air tight container or resealable storage bag surrounded by napkins. The air-tight container helps keep the muffins moist. The napkins will absorb any moisture the muffins release to prevent them from being soggy.

Muffin tin filled with Double Chocolate Cream Cheese Muffins next to chocolate chips.

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Plate of gluten & dairy free Double Chocolate Cream Cheese Muffins next to chocolate chips, cacao powder, linen napkin, tin of muffins, and cross sections of muffins.
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📖 Recipe

Close up on a Double Chocolate Chip Cream Cheese Muffin with muffins, muffin tin, chocolate chips, and cacao powder in the background.

Double Chocolate Cream Cheese Muffins {Gluten Free and Dairy Free}

Katie AdamsKatie Adams
These muffins' combination of bittersweet chocolate and tangy sweet cream cheese will tame your fiercest chocolate craving!
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 23 minutes mins
Total Time 38 minutes mins
Course Breakfast, Dessert, Snack
Cuisine American
Servings 15
Calories 363 kcal

Equipment

  • 1 large mixing bowl
  • 2 Medium mixing bowls
  • 1 Whisk
  • 1 Wooden spoon or silicon spatula
  • 1 hand mixer
  • 2 12 cup muffin pans
  • muffin liners

Ingredients
  

Dry Ingredients

  • 1½ cups almond flour
  • ½ cup oat flour
  • 1 cup brown rice flour
  • ½ cup cacao powder
  • 1½ teaspoon baking soda
  • 1½ teaspoon xanthan gum
  • 2 pinches salt
  • 1 cup white sugar*
  • 1 cup allergy friendly chocolate chips**

Wet Ingredients

  • 1½ cup almond milk or other dairy free milk
  • ½ cup neutral oil
  • 3 whole eggs
  • 1 tablespoon pure vanilla
  • 1½ tablespoon apple cider vinegar

Cream Cheese

  • 4 oz dairy-free plain cream cheese***
  • 6 tbps white sugar
  • 1 whole egg
  • 1 egg white

Instructions
 

Muffin Batter

  • Pre-heat oven to 350°. Place muffin liners in muffin pans.
  • In medium mixing bowl combine dry ingredients: almond flour, oat flour, brown rice flower, cacao powder, baking soda, xanthan gum, salt, and sugar. Whisk to combine.
    Dry ingredients for double chocolate cream cheese muffins in medium glass mixing bowl beside a whisk.
  • In large mixing bowl combine wet ingredients: almond milk, neutral oil, whole eggs, apple cider vinegar, vanilla. Whisk until well combined.
    Wet ingredients for double chocolate cream cheese muffins in a large mixing bowl.
  • Combine dry ingredients into wet ingredients and whisk until well combined and smooth. Batter will be thick.
    Double chocolate cream cheese muffin batter inside a large mixing bowl
  • Mix chocolate chips into batter.
    Double chocolate cream cheese muffin batter with chocolate chips in large mixing bowl.
  • If using a piping bag: Place the batter in a large 21" piping bag (or large zip-topped bag with the end cut off).

Cream Cheese Filling

  • In medium bowl add dairy free cream cheese and sugar. Blend on MED-LOW until well combined and smooth. Add egg and egg white. Blend on MED until well combined and smooth.
    Dairy free cream cheese, whole eggs, and maple sugar each in a glass bowl.
  • If using a piping bag: Add the cream cheese filling in a 16" piping bag (or small zip-topped bag with the end cut off).

Muffin Cream Cheese Mixture

  • Using either a large piping bag/zip-topped bag, or scantly filled ice cream scoop, fill muffin tins a little over ⅔ full. Use the back of a spoon to make a well in each one.
    Muffin tins with liners filled ⅔ full with Double chocolate cream cheese muffin batter.
  • Use a spoon to carefully push the muffin batter the the sides to create a well in the middle. The batter is pretty thick so it will stay where you push it.
    Muffin tin with double chocolate cream cheese muffin batter with wells spooned in the middle.
  • Use a small piping bag or spoon to fill each well with cream cheese filling.
    Muffin tins filled with Double chocolate cream cheese muffin mixture.
  • Using a large piping bag or spoon top each muffin with more batter. It's ok if the cream cheese filling is oozing out some.
    Double Chocolate Cream Cheese Muffins unbaked in a a baking pan.
  • Bake 23-24 minutes until the cream cheese is set and a toothpick inserted into center of muffin comes out clean or with scant crumbs.

Notes

*Feel free to use cane sugar if you prefer. I’ve noticed that cane sugar doesn’t sit well with my family. So, this is the maple sugar and coconut sugar I typically use. All maple sugar is pricy, but this version doesn’t clump as badly as other brands I have tried. I typically use it in lighter colored baked goods (vanilla cakes, lemon baked goods, streusel/crumble/crisp toppings etc). That said, I use coconut sugar more often due to affordability. It darkens then end product, but if it’s just my family eating it we don’t mind!! 
**These are my favorite allergy friendly chocolate chips. They taste great and are artificial sugar free. 
***I like kitehill  or Miyoko’s brand cream cheese. Dairy free cream cheeses tend to contain more liquid so make sure to drain any excess before using. Be aware, both these brands do contain nuts. Violife makes a nut free, dairy free cream cheese, however I have never used it. I do eat a lot of their dairy free, nut free cheese products and the quality is always very good. 
*Recipe was improved and updated September 2024 based on feedback*

Nutrition

Serving: 1muffinCalories: 363kcalCarbohydrates: 39gProtein: 7gFat: 22gSaturated Fat: 4gPolyunsaturated Fat: 1gMonounsaturated Fat: 6gCholesterol: 1mgSodium: 369mgPotassium: 147mgFiber: 5gSugar: 20gVitamin A: 1IUCalcium: 96mgIron: 2mg
Keyword chocolate, cream cheese, dairy-free, gluten-free, muffin, soy-free
Tried this recipe?Let us know how it was!

*Post was updated September 2024. Recipe was improved and updated September 2024 based on feedback.

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@ Joyfully Full 2024

Welcome!

Katie AdamsHi! I’m Katie Adams in Columbus Ohio and I’ve been cooking tasty, allergy friendly meals since 2013 and began creating original recipes shortly after that. I’m so happy to be able share my family meals with you!

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