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Gluten Free Chocolate Chip Streusel Muffins

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A small batch of chocolate chip gluten free streusel muffins make breakfast a little sweeter!  A flavorful almond flour blend combines with sour cream and a healthy amount of chocolate mini chips.  The result is muffins with an abundance of flavor, the perfect muffin texture, and a delicious caramelized streusel topping. 

Soft inside of a chocolate chip gluten free muffins dotted with tons of chocolate chips.

Gluten Free Chocolate Chip Muffins with Streusel Topping

I took my traditional chocolate chip muffins and gluten free naturally sweetened chocolate chip muffins recipes to make this small batch of breakfast muffins.  While they still have the same soft and sturdy texture of both, these particular muffins are gluten free and made with cane sugar.

And while I love to use natural sweeteners in my baking recipes – like maple syrup in the gluten free maple bread, or sucanat in the almond coffee cake, I wanted a classic recipe that uses more in-your- pantry ingredients.

The goal for this muffin recipe is to create a base for any great muffin.  For example, the gluten free blueberry muffins are essentially this recipe, but with blueberries – of course.  And, we achieve that here.  Plus, the added bonus is we now have a streusel muffin topping we can put on just about anything!

What Makes These Muffins Great

  • They don’t taste gluten free! – A primary goal in all my gluten free recipes is to make sure you can’t tell that they are gluten free.  Which I give credit to the flavorful flour blend I use with almond flour as the base.
  • Soft and sturdy – A good muffin should be able to withstand a dunk in coffee, or being hand held without a mess.  That is these muffins.  Yet, their sturdy texture is also incredibly soft and moist.
  • Easy – The small batch recipe already implies easy.  However, we use relatively easy to source ingredients, and some that you may already have on hand!
  • The streusel topping! – I love a good streusel – on my coffee cake, pumpkin muffins, and these chocolate chip delights.  The streusel bakes into a caramelize bite – full of buttery sweetness.
  • Versatile – Now that we have a base muffin recipe, we can change up the flavors and add-in’s – observing caution of course.  Fruit, nuts, different flavor extracts, or even sprinkles won’t alter the muffin batter and still give you one tasty treat!
Three neatly stacked gluten free chocolate chip muffins stacked on a table.

Everything You Need To Make Gluten Free Streusel Muffins


  • Almond Flour – I recommend blanched almond flour because it is ground finer and without the skins.  The almond flour provides structure, flavor, and moisture to the muffins.
  • Sweet Rice Flour – Sweet rice flour works as a binder in the muffins, similar to how gluten works in traditional baking.  It provides a soft and tender texture.
  • Tapioca Flour – Tapioca flour adds chew to the muffins and helps make them soft.
  • Coconut Flour – Coconut flour is absorbent and I like to use to balance all of the wet ingredients.
  • Baking Powder – For texture and lift in the muffins.
  • Salt – Salt balances and enhances flavor.
  • Sugar – My preference is organic cane sugar because of its caramel flavor and it isn’t as processed as white granulated sugar.  However, you can use granulated sugar if you prefer.
  • Sour Cream – Sour cream is key in these muffins to add texture and moisture.  And it should be full fat sour cream to get all the benefit.
  • Coconut Oil – I like to use coconut oil to keep the muffins moist longer.  You can use melted butter – just note the muffins may only stay moist for about 1 to 2 days.
  • Egg – 1 large egg.
  • Vanilla – For flavor!
  • Chocolate Chips – My preference is mini chips because you get a wider distribution and they are less likely to sink.  Similar to how the chips stay floating in the gluten free chocolate chip mini loaf.

Baking Equipment

  • Mixing Bowls
  • Muffin Pan with Liners
  • Cookie Scoop – I like to use a medium cookie scoop to portion the batter equally, and it is less messy!
Pretty breakfast muffins on a small wooden plate.

Tips For chocolate chip streusel Muffins Success

  • Use mini chocolate chips – The smaller chips are great bites of texture in the muffins and you get more in each bite!  Plus, they are less likely to sink to the bottom of the muffins.
  • Use full fat sour cream – To get soft and moist muffins.  Otherwise, low-fat sour cream or yogurt may not yield the same result.  That said, you can try Greek yogurt because of its fat and protein content.
  • Don’t stress the streusel – Because the ingredients are so few and don’t include any tricky items (i.e. eggs, leaverners), we simply want to create a crumbly dough.
  • Let the batter rest before baking – This allows the flours to hydrate.  Otherwise, the muffins may be a bit crumbly if you don’t give the batter time to rest.
  • Add a few extra chocolate chips to the top – Before baking, you can add a few more mini chips to the tops of the muffins – just because!  Either before or after the streusel – totally your preference.
  • Allow the muffins to cool completely – Gluten free baked goods always taste better when they are completely cool.  It’s almost as if the flavors continue to develop as they cool.
A lovely stack of breakfast muffins on a table.

FAQ’S: Gluten Free Chocolate Chip Muffins with Streusel Topping

Can this recipe be doubled?

I haven’t teste a larger batch, so can’t say for certain. But if you do, let us know how it worked!

Will a 1:1 or cup-4-cup gluten free flour work instead?

Probably not. The blends are vastly different than mine and I find they bake drier. All of the other ingredients and ratios would likely need to be adjusted.

Why butter in the streusel, and not in the muffin batter?

I prefer how the butter and sugar caramelize to make the streusel topping. However, you can swap in butter in the muffin batter OR coconut oil in the streusel. Notes are in the recipe for this.

What happens if I don’t let the batter rest before baking?

The muffins may turn out crumbly. Letting the batter rest – especially gluten free batter – allows the flours to hydrate and flavors develop. Not dissimilar to a traditional croissant recipe!

How should I store leftovers?

The muffins will stay moist covered at room temperature for 2 to 3 days.

Chocolate chip gluten free muffins stacked on a wire cooling rack.

Gluten Free Chocolate Chip Streusel Muffins

Yield: 4 Muffins
A small batch of chocolate chip gluten free streusel muffins make breakfast a little sweeter!  A flavorful almond flour blend combines with sour cream and a healthy amount of chocolate mini chips.  The result is muffins with an abundance of flavor, the perfect muffin texture, and a delicious caramelized streusel topping.  
Prep10 minutes
Cook22 minutes
Total32 minutes


  • 1 – Muffin/Cupcake Pan


Muffin Streusel Topping

Gluten Free Chocolate Chip Muffins


Muffin Streusel Topping

  • In a small mixing bowl, whisk together the almond flour, tapioca flour, sugar, and salt. Add the butter cubes, and using your fingers or a fork, cut the butter into the flour and mix until the dough is moist and you have streusel crumbs. Refrigerate until ready to use.
    2 ½ tablespoons blanched almond flour, 2 tablespoons tapioca flour, 2 tablespoons organic cane sugar, pinch salt, 1 tablespoon unsalted butter, cut into cubes

Gluten Free Chocolate Chip Muffins

  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Line a muffin/cupcake pan with 4 muffin liners.
  • In a small mixing bowl, whisk together the almond flour, sweet rice flour, tapioca flour, coconut flour, baking powder, and salt.
    5 tablespoons blanched almond flour, 3 ½ tablespoons sweet rice flour, 1 tablespoon tapioca flour, 1 tablespoon coconut flour, ½ teaspoon baking powder, ¼ teaspoon salt
  • In a medium mixing bowl, add the sugar, sour cream, coconut oil, egg, and vanilla extract. Whisk until incorporated and smooth.
    ¼ cup organic cane sugar, 2 tablespoons full fat sour cream, room temperature, 1 tablespoon cold pressed refined coconut oil, melted, 1 large egg, room temperature, 1 teaspoon vanilla extract
  • Sprinkle the dry ingredients over the wet, and stir until no dry streaks remain. Fold in the chocolate chips until just mixed in.
    ¼ cup chocolate chips, any kind
  • Scoop the batter into equal portions into the prepared muffin liners. The liners will be about 90 percent full. Sprinkle the streusel crumbs over the tops of the muffins. Let the muffins sit for 5 minutes before baking to give the batter time to hydrate. Otherwise, the muffins may turn out crumbly. Tip Dot a few more chocolate chips on the tops of each muffin before or after adding the streusel, if you want extra chocolate chips at the top.
  • Bake the muffins for 20 to 22 minutes, or until the edges are golden, the muffins are springy to the touch, and a toothpick inserted in the middle comes out mostly clean. Cool in the pan set on a wire rack for 10 minutes – then transfer the muffins to the wire rack to cool completely. Enjoy!
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  • Sour Cream – I recommend full fat sour cream to give the muffins their moist and tender texture.  You can swap in Greek yogurt.
  • Butter in the Streusel – I prefer butter in the streusel topping for the flavor and how it combines with the sugar to caramelize.  You can swap in coconut oil.
  • Chocolate Chips on Top – Before baking, add a few extra chocolate chips on top of each muffin before or after adding the streusel.
  • Rest the Batter – I like to let gluten free batters with sweet rice flour rest a few minutes before baking.  This gives the batter time to hydrate and the end result won’t be too crumbly.
  • 1:1 Gluten Free Flour – I have not tested this recipe with a 1:1 gluten free flour blend.  I would recommend following the recipe for chocolate chip muffins and swap the flour 1:1.
  • Naturally Sweetened Muffins – If you prefer to use a natural sweetener I have a chocolate chip gluten free muffin recipe that uses a paleo flour blend and coconut sugar.   
  • Storing Leftovers – The muffins will stay moist covered at room temperature for up to 2 days.  Beyond that, they may start to dry out.
Course: Breakfast
Cuisine: American
Author: Erin Cernich


Calories: 343kcal | Carbohydrates: 41g | Protein: 5g | Fat: 19g | Saturated Fat: 8g | Polyunsaturated Fat: 0.5g | Monounsaturated Fat: 2g | Trans Fat: 0.1g | Cholesterol: 58mg | Sodium: 223mg | Potassium: 71mg | Fiber: 2g | Sugar: 26g | Vitamin A: 192IU | Vitamin C: 0.1mg | Calcium: 82mg | Iron: 1mg
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you!

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