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These Gluten-Free Coffee Cake Muffins are fluffy, moist, and packed with good-for-you ingredients. Made with a combination of almond, coconut and tapioca flour, this gluten-free muffin recipe is grain-free, made with unrefined sweeteners, and is the perfect grab-and-go breakfast!

Gluten Free coffee crumb cake muffins

Gluten-Free Coffee Cake Muffins

These grain-free muffins are so simple, moist, and delicious. They have a light and fluffy texture and the perfect cinnamon crumble topping. Nobody will know these muffins are gluten-free, grain-free, and paleo-friendly! These muffins are an OG Lexi’s Clean Kitchen and still a goodie all these years later! This recipe was originally published back in 2014, but we are sharing today with a slightly updated recipe and new photos so more of you can find it!

These are perfect to make as the weather starts to cool down, to be enjoyed on a crisp fall morning with a cup of coffee (or tea) in hand!

Coffee crumb muffin batter in a bowl.

Ingredients Needed

  • Almond Flour
  • Coconut Flour
  • Tapioca Flour
  • Eggs
  • Honey or Maple Syrup
  • Unsweetened Applesauce
  • Vanilla Extract
  • Baking Powder and Soda
  • Cinnamon
  • Butter or Coconut Oil


Flour: Unfortunately, for gluten-free baking that does not use a gluten-free flour blend, it can be really tricky to substitute in different flours in place of the ones called for in the recipe. In this case, we call for almond flour, tapioca flour and coconut flour. We never call for 3 different types of flour for a recipe unless it was absolutely essential for the texture, and that is the case with this recipe. At this time, we can’t recommend any substitutes for the flours called for. But we do have plenty of muffin recipes on the site that use a different variety of flours, such as oat flour muffins, in case there is a nut allergy in the family.

Butter: We loved the flavor of this muffin with butter, but it can easily be swapped out for softened room temperature coconut oil.

Applessauce: The applesauce should not be replaced in this recipe, as it’s crucial for the texture as well as the moisture level.

Eggs: We haven’t tried it, but this recipe may work with 2 flax eggs.

How to Measure Almond Flour

If you have an electronic kitchen scale at home, it’s best to use it here to measure almond flour. Almond flour can be tricky to measure as it can be easily compacted, even straight from the bag. The same goes for coconut flour because such a small difference in measuring can impact a recipe because it’s such an absorbent flour. So we’ve included the weight in grams here. Any electronic kitchen scale can switch between grams and ounces, and grams are more precise so we’re offering that. If you don’t have a scale: lightly scoop the almond flour or coconut flour into the cup measurement and level it off.

Gluten Free Coffee Cake Muffins before being baked in a muffin tin.

Troubleshooting a Crumb Topping

Sometimes it can be tricky to get just the right crumb topping consistency! This recipe calls for softened butter (or coconut oil) to be added to almond flour and tapioca flour. It might feel a little funny adding softened butter to a dry flour, but it works out really well. This recipe also calls for maple syrup, and we don’t recommend switching out this sweetener as it makes it essential for the crumbly topping.

If for some reason your crumble isn’t very crumbly and is too wet, you can add in a tablespoon each of tapioca and almond flour until it reaches the correct consistency of a soft crumble.

If for some reason your crumble isn’t very crumbly and is too dry, you can add in a teaspoon more maple syrup until it reaches that crumbly consistency.

Want to Make it as A Coffee Cake?

We heard you! You also want to be able to bake this as a coffee cake. Good news, it’s pretty much the same recipe! Instead of baking in a muffin tin, add the batter and crumble topping to a greased 8 x 8 inch baking dish. Bake in the center rack for 30-35, or until a toothpick inserted in the center of the cake comes out clean with just moist crumbs.


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Coffee Crumb Cake Muffins

5 from 2 votes
These Gluten-Free Coffee Cake Muffins are fluffy, moist, and packed with good-for-you ingredients. Made with a combination of almond, coconut and tapioca flour, this gluten-free muffin recipe is grain-free, made with unrefined sweeteners, and is the perfect grab-and-go breakfast!
Servings 12 Muffins
Prep Time 10 minutes
Cook Time 28 minutes


For Muffin Base:

  • 2 eggs
  • 1/3 cup honey or maple syrup
  • 1/4 cup unsweetened applesauce
  • 1 teaspoon vanilla
  • 2 cups 192 grams almond flour
  • ¼ cup 28 grams coconut flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon cinnamon
  • 1/8 teaspoon salt
  • ¼ cup unsalted butter softened, or coconut oil
  • Crumb Topping
  • 1 cup 98 grams almond flour
  • ¼ cup 30 grams tapioca flour
  • 1/2 teaspoon ground cinnamon
  • 2 tablespoons maple syrup
  • 2 tablespoons unsalted butter softened, or coconut oil


  • Preheat oven to 350ºF and line a 12 cup muffin tin with silicone or parchment paper liners.
  • In a large bowl add eggs, sweetener, apple sauce and vanilla and whisk together to combine.
  • Add in the almond flour, coconut flour, baking powder, baking soda, cinnamon, salt, and softened butter and mix with a spatula until smooth. 
  • Make the streusel: Combine almond flour, tapioca flour, cinnamon, maple syrup and softened butter together in a bowl. Mix together until the mixture is crumbly.
  • Fill each muffin cup ¾ full. Top each muffin with about 1 heaping tablespoon of the streusel.
  • Bake in the middle rack for 18-20 minutes, or until the muffins spring back when touched.
Keyword: Gluten-free Coffee Cake Muffins
Course: Breakfast
Method: Bake
Author: Lexi's Clean Kitchen

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  1. These. Look. Amazing. Running to my kitchen right now to try them. Thanks for the great recipe!

  2. I made these for my daughter’s end of the year breakfast picnic, and they were a huge hit! One person told me they were the best gluten-free baked good they had ever had (and, she’s gluten-free, so it’s not like she had no comparison). I think five different people asked me for the recipe. I love that the muffin itself is not sweet, so that the buttery, sugary crumb topping is still relatively guilt-free!

    1. This post made my day, Lee! I am so glad they were a huge hit 🙂 Thanks for taking the time to write.

  3. Yum! Pantry is still “converting” so I used sweetened shredded coconut for the topping.
    Super moist muffins.

  4. I’m just now seeing this as a recipe on another blog and for once I actually have all the ingredients on hand. 🙂 I’m so excited now to make these. Thanks so much

  5. So glad I read through the comments as I was just about to make these with almond meal/flour. I had no idea there was a difference 🙁 back to the store. Hope I can find it!

  6. These are amazing! I’ve already made them twice. The only issue I keep having is getting an even distribution of my topping, it’s too wet to make it even and then as they cook, my muffins cave in! They still taste great but aren’t nearly as pretty.

  7. Lexi, I love your recipes! I made these with almond meal/flour and didn’t work so well 😉 however I can’t find pure almond flour anywhere! Where do you buy yours (assuming you’re not baking with almond meal/flour combo)??

  8. Just made these…they turned out amazing! It’s so refreshing to find Paleo recipes that don’t require a million (weird) ingredients, are easy, and turn out good! Just batched cooked three meals from this webpage and they ALL turned out delicious. So grateful for your ideas Lexi. Thank you!

  9. I totally love these muffins for breakfast (one of my favorite breakfast foods) or a afternoon pick me up. I know they have to taste amazing!

  10. Perfect! We have an absolutely amazing coffee cake recipe handed down to us from my husbands family but it is so not gluten free or paleo for that matter. Totally trying this one to see how it compares, can’t wait! 🙂 Thanks Lexi!

  11. Those look amazing! Coffee crumb cake is one of my favorites! A special treat that I love to enjoy, but do not get to have it too often! Even better that it is paleo! Yum! Thanks Lexi!

  12. When I went GF the one thing that I missed the most was my mom’s coffee cake, this looks just like them and I can’t wait to try your recipe out!

  13. I made your Cioppino Stew this past weekend, and it was soooo good! I adapted the ingredients a bit since I’m allergic to scallops and made it in the crockpot. The result was truly amazing. Been saving a bunch of your recipes and this is the first one I tried — thank you so much for all the great-tasting, healthy food ideas! Will be making these muffins soon.

  14. Lexi, what if you absolute cannot stand coconut flour? Could I use more almond flour instead? Is there any substitute? Thanks!

  15. Love the nutritional stats on these muffins compared to one you would find in a bakery or coffee shop! Pinned for later.