Gluten free Chocolate Coffee Cake Muffins

Gluten free Chocolate Coffee Cake Muffins are packed with chocolatey goodness.

These are one of the most indulgent treats I’ve made and shared on the blog. They are chocolate, chocolate, chocolate to the max. Cocoa is added to the batter as well as chocolate chips. Then the top crumble has more cocoa and both mini chocolate chips and white chocolate chips.

The rich chocolate is cut slightly with a layer of cream cheese filling between the two layers of chocolatey goodness.

These gluten free chocolate coffee cake muffins (say that three times fast!) are perfect when that chocolate craving strikes. The inside is perfectly moist and cakey. When eaten warm the chocolate chips inside the cake are gooey and satisfying. The cream cheese layer and the chocolate crumble topping pair beautifully together and provide contrasting texture.

When you bite into it you get the creamy cake, smooth cream cheese and lightly crunchy crumble. It’s the perfect trifecta of texture and flavor that your taste buds will love.

I’m a little obsessed and have a few in the freezer for when the mood strikes.

I use a muffin pan to make these guys, not a standard cupcake pan. They are a bit bigger than a cupcake pan and usually have 6 cups vs the 12 cups of a cupcake pan. This way the muffins are indeed muffin size (think Costco muffins). You can try making them in a cupcake pan but the ratios may be different and the cooking time will be less.

If coffee cakes are your thing you should check out my Pumpkin coffee cake and my regular coffee cake muffins.


Chocolate Coffee Cake Muffins

Chocolate batter, chocolate chips, and chocolate crumble with a swirl of cream cheese frosting make these Chocolate coffee cake muffins extra rich.

  • Prep Time: 10 minutes
  • Cook Time: 30 minutes
  • Total Time: 50 minutes
  • Yield: 6 1x
  • Category: Breakfast, Dessert
  • Cuisine: American


Units Scale
  • 1 Egg
  • 1/4 cup White Sugar
  • 1/4 cup Brown Sugar
  • 1/2 cup Greek Yogurt
  • 2 TBS Oil (Avocado or Olive oil)
  • 2 TBS Butter (Melted)
  • 3 TBS Milk
  • 1/2 tsp Vanilla Extract
  • 1 cup Bob's red mill 1 to 1 gluten free flour
  • 1/4 tsp Baking soda
  • 1/2 tsp Baking powder
  • 1/4 tsp Salt
  • 1/2 cup Dutch Cocoa powder
  • 1/2 cup Chocolate Chips

Cream cheese layer

  • 4 oz Cream Cheese
  • 1 Egg
  • 3 TBS Sugar

Crumble topping

  • 1/2 cup Bob's red mill 1 to 1 gluten free flour
  • 1/4 cup Brown Sugar
  • 1/4 cup Butter
  • 1/4 cup Dutch Cocoa powder
  • 1/4 cup Mini chocolate chips
  • 1/4 cup White Chocolate chips


  1. Preheat the oven to 350F and place paper liners in a Large 6 pan muffin tin
  2. In a stand mixer combine the egg, sugars, Greek yogurt, oil, butter, milk and vanilla.
  3. In a separate bowl whisk together flour, baking soda, baking powder, salt and Cocoa powder.
  4. With the stand mixer on low slowly add the dry ingredients to the wet. Once fully combined mix in the chocolate chips.
  5. Divide this batter between the muffin tins.
  6. In another bowl combine the cream cheese, egg, and sugar. It's okay if it's a bit lumpy. Divide this out on top of the batter filled cups.
  7. In another bowl combine the flour, sugar, butter, and cocoa powder to make the crumble. I like to mix it and form a handful into a small log in my hand. It will come together but be easily crumbled. Crumble half of this over the cream cheese layer.
  8. Combine the mini chocolate chips and white chocolate chips together and sprinkle over the first layer of crumble. Then sprinkle the rest of the crumble over the top.
  9. Bake the muffins for 25-30 minutes until the center batter is fully cooked.
  10. Let rest for 10 minutes before moving to a cooling rack. Once cool serve with coffee or milk.

Keywords: Baked, Breakfast, Brunch, Chocolate, chocolate cake, coffee, coffee cake, cream cheese, cupcakes, dessert, Gluten free, gluten free cake, Muffins

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Alycia Louise
Alycia has worked in the food industry for over 10 years. She lives in the PNW with her husband and three dogs. Her likes include coffee, rainy days and horror movies.
Articles: 251


    • Hi Vanessa,
      Thanks for the question. I find that they keep 2-3 days after baking before getting that ‘day old’ texture and loss of flavor. Unless I’m making them for a party I always freeze whatever I don’t think we will get to in time. They freeze well and thaw out beautifully.

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