Chocolate Chip Marble Muffins

When you can’t decide between chocolate and vanilla, try these gluten free chocolate chip marble muffins. Moist, tender, easy to make and the perfect balance of both flavors in every bite.

I think these gluten free marble muffins are my new favorite muffin recipe. They’re the perfect balance of sweet, fluffy, indulgent from the chocolate but still have a generous 6 grams of protein per muffin thanks to the greek yogurt and eggs.

Marble desserts can seem intimidating, but this is actually a very easy recipe to follow. Just make your base chocolate chip muffin batter, then set some aside to make the chocolate and scoop them together. That’s it! If you love this recipe, try my raspberry chocolate chip muffins or marble bundt cake next!

Quick tips

• I used Bob’s Red Mill 1:1 Baking Flour here, but another gluten free blend should work just fine as long as it has xanthan gum. I do not recommend almond flour, coconut flour, oat flour etc.
• When it comes to swirling the vanilla and chocolate batters- there really isn’t a right or wrong approach! You can swirl them together a lot, or just scoop and leave them more separate, just depends on your preference and the look you’re going for. I prefer more distinct sections so the chocolate flavor doesn’t get diluted.

How to make gluten free marble muffins

Preheat the oven to 350 and line a 12 cavity muffin tin with liners and set aside. In a medium mixing bowl, whisk together the melted butter, white sugar and brown sugar.

Whisk in the eggs, greek yogurt, milk and vanilla extract until smooth. Whisk in the gluten free flour, baking powder, baking soda and salt. Mix in the chocolate chips.

Scoop out 2 1/2 cups of batter into a second bowl. Whisk in the cocoa powder and milk.

Use a spoon to alternate scooping the vanilla and chocolate batter into a muffin tin. There really isn’t a right or wrong method here, you can leave more distinct sections or swirl them together a bit.

Top with extra chocolate chips and bake for 20-24 minutes or until a toothpick comes out clean. Let cool for about 20 minutes before serving and enjoy!

Key ingredients & swaps

Eggs. Two eggs help make these marbles muffins nice and fluffy and bind all ingredients together. I don’t recommend any swaps here since these are such a key ingredient for the proper texture!

Sugar. A mix of white and brown sugar will sweeten the muffins and add some moisture. You can swap for coconut sugar for a refined sugar free option, but I do not recommend any liquid sweeteners here.

Butter. A bit of butter helps add a lot of moisture to these gluten free muffins and gives them a nice fresh from a bakery like flavor!

Greek yogurt. I love using greek yogurt in baking because it adds moisture and the high protein content gives a fluffy texture. You can swap for a dairy free version like Kite Hill Greek Style Yogurt if you need/prefer. I like full fat greek yogurt, but any kind will work. I suggest a plain and unsweetened.

Milk. I used regular cow’s milk because that’s what I have on hand, but any kind of milk, either dairy or non-dairy will work here.

Cocoa powder. You want a good quality cocoa powder to ensure the chocolate portion of the muffin has a rich flavor.

How to store and freeze

Once prepared, these gluten free marble muffins will keep in the for about 3 days at room temperature. However, I like to store them in the fridge so they last up to 5 days. I’ll then reheat in the microwave so they have a good as new texture.

You can also freeze these muffins after baking! Just let them cool completely, then transfer to a freezer safe bag. Freeze for up to 2 months, then reheat in the oven until warm through the center. I like to freeze without the wrapper.

More muffin recipes you will love!

• Matcha Muffins
• Lemon Poppyseed Muffins
• Carrot Cake Muffins
• Blueberry Protein Muffins

Be sure to follow along on on instagram and subscribe to my email list for more recipes and updates. Leave a comment and rating below if you try this recipe and let us know how it turns out!