This post may contain affiliate links. Please read my disclosure policy.

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.


Watch the video here:

If you like this muffin recipe, check out these:

Pin this recipe to save it for later!

Pin it!

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

You May Also Like

Secrets to Quick Dinners
Get my practical tips & advice for a healthier life dropped right into your inbox!
newsletter collage

Leave a Comment

Your email address will not be published. Required fields are marked *

Recipe Rating


  1. Just taste tested my first batch of these! Winner! Easy and enjoyable. I’ll definitely be making these for my daughter in love’s baby shower.

  2. 5 stars
    Made theses for my friends this weekend and they were so good! I whipped them up in no time and had warm tasty muffins for when they woke up. The recipe is simple and packs a lot of flavor. Would be good if you wanted to add fruit too like blueberries or raspberries. May try that next time. Love these recipes.

  3. 5 stars
    This was amazing! I made it in an 8×8 pan and sprinkled just a little bit of coconut sugar over the crumble for a little added sweetness (so that my kids would definitely eat it). Perfection!

  4. Yum!! If I wanted to make this in a bunt pan instead of muffins (to make it more of a coffee cake), what would you recommend the cooking time be adjusted to?

  5. Hi Lexi! I’m dying to try these muffins but have a bad almond allergy…thoughts on substitutions? I have tapioca flour, coconut flour and arrowroot flour. Let me know what you think and suggestions for how much if you have an idea!

  6. Hi Lexi! These look amazing – I’ve never made coffee cake muffins before, only coffee cake … do you think I could make this recipe in a cake pan, either a square one or a bread loaf pan? How do you think it would bake?

  7. I have a weekly baking club with my 5 & 7 year old nieces. I usually let the girls pick their own recipes but today they let me pick the recipes. I am just about finished with my first Whole30 and decided I would freeze the muffins as my first treat next week. The recipe was easy to follow but I could only make 9 as there was not enough batter for the 10th one. They are on the smaller size after baking but smelled so good. My niece said they were delicious.