Soft & fluffy almond flour pumpkin muffins that are naturally gluten free! You'd never guess these are made with good-for-you ingredients, like no refined sugars or oils. A healthy and family-friendly fall you treat you can feel good about.
Looking for more healthier fall recipes? Try these pumpkin breakfast cookies and easy gluten-free pumpkin scones next.

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"Love these healthier pumpkin muffins! We've been having them for breakfast this week." - Janessa
Why You'll Love These Almond Flour Pumpkin Muffins
- Made with real food ingredients. You'll love that these almond flour muffins are made with grain-free ingredients and naturally and lightly sweetened with coconut sugar.
- Better than store-bought snacks. Each muffin has 6 grams of protein and 3 grams of fiber. Way more than most store-bought snacks, so go ahead and enjoy these with coffee or as an afternoon snack, and don't feel bad if you accidentally eat two.
- Paleo friendly. While I'm not Paleo, I love the Paleo approach to eating since it's all clean food and that's what I'm all about. Try these Paleo blackberry muffins or Paleo donuts if you'd like to try more Paleo baking recipes.
Fall is in the air and that means all things pumpkin spice. These almond flour pumpkin muffins have the most incredibly soft and fluffy texture, thanks to the combination of almond flour, tapioca flour, and coconut flour.
Almond flour on its own can have a denser texture, but with the combination of flours, you get the nice soft texture you'd expect with a muffin made with wheat flour, while still keeping them gluten-free. Can't wait for you to try these ones!
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Ingredient Notes

- Almond flour- Use almond flour/blanched almond flour and not almond meal. Blanched almond flour uses almond with the skin removed and is more finely ground. This will result in lighter and fluffier muffins. I like Terrasoul because it's organic. But I've also had good luck Bob's Red Mill almond flour.
- Pumpkin puree- Be sure to use pumpkin puree and not pumpkin pie mix. The only ingredient should be pumpkin.
- Tapioca flour- This can also be called tapioca starch. If in a pinch, arrowroot starch can be used. However, I believe tapioca flour works best.
- Non-dairy milk- Make sure to use plain and unsweetened non-dairy milk. If not dairy free, you can use regular cow's milk.
A complete list of ingredients can be found in the recipe card below. The above are some specific notes to help with selecting ingredients.
💚Clean food tip: Look for dairy-free milk that contains just the source of the milk (i.e., almonds), water, and maybe salt. Avoid gums and additives if you can. Malk and Elmhurst are my favorites.
Variations
- Make mini-muffins instead of full sized muffins. Grease a 24-cup mini muffin pan and divide batter between muffin cups. Bake at 350F for 12-15 minutes, or until set and a toothpick inserted in center of muffins comes out clean. I also have a great recipe for gluten-free mini muffins if you'd like to check those out.
- Fold ½ cup - ¾ cup chocolate chips into the batter for pumpkin chocolate chip muffins (or give my gluten-free chocolate chip pumpkin bread a try). If needing these to be Paleo, use Paleo compliant chocolate chips.
- Sprinkle some pumpkin seeds on the top of muffins before baking for some crunch and added nutrients. Or, add some chopped walnuts or pecans on top or mix in with the batter.
- Replace ¼ cup of the almond flour with ground flaxseeds for an extra nutrient boost.
How To Make

Step 1: Combine the dry ingredients in a large mixing bowl.

Step 2: Make a well in the center of the dry ingredients and add the wet ingredients. Whisk to combine.

Step 3: Fully mix the wet ingredients in with the dry ingredients.

Step 4: Lightly grease, or line a 12-cup muffin tin with liners. Evenly divide the muffin batter between the 12 muffin cups.

Step 5: Bake at 350-degrees F for 24-27 minutes.
Expert Tips for the Best Almond Flour Muffins
- When measuring almond flour, scoop flour into measuring cup and level off with a knife. Do not pack the flour into the measuring cup or you'll end up with too much and your muffins may be dense and dry.
- Do not overmix the batter. Almond flour can release extra oil as its mixed, which could result in soggier muffins.
- For a rounder muffin top, use a large spring-loaded cookie scoop (¼ cup size) when transferring batter to the pan.
- I prefer to lightly grease my muffin pan instead of using liners, but if you do use muffins liners, wait for muffins to fully cool before tearing the liners off, or else the liners will stick to the muffins.
- Let muffins cool to room temperature. Almond flour baked goods continue to set as they cool. If you can, wait to dig in. If you can't wait, know that as they cool, the flours will continue to absorb moisture and the muffins will fluff up a bit.
Did you know?? Almond flour should be stored in the fridge or freezer once opened to maintain freshness.

Storing
Storing: These Paleo pumpkin muffins taste best within the first two days. Keep leftovers in an airtight container in the fridge to extend freshness - they will stay fresh for 4-5 days when kept in the fridge. If you'd like, warm them up in the microwave for 10 seconds before eating.
Freezing: These can also be frozen in a freezer safe container for up to 3 months.
Recipe FAQs
I have not tried an egg substitute, but I do know almond flour can be tricky when baking with flax eggs or other egg substitutes. If you do try, please let me know how they turn out.
This is typically due to the fact that the muffins haven't cooled completely. Another reason could just be your liners - try using parchment paper liners or silicon liners as those can prevent sticking as well.
Overmixing or incorrect measuring of ingredients can cause dense muffins. Using fresh almond flour also helps to create a lighter texture.

More Healthy Fall Recipes to Try!
If you make this recipe, please let me know what you think! I would so appreciate you leaving a star rating and/or comment below. And don't forget to share a photo on Instagram or Facebook and mention @CleanPlateMama!
Eat Clean.Be Well!
-Sara
Almond Flour Pumpkin Muffins
Save This Recipe For Later!
Equipment
- 1 large mixing bowl
- 1 12-cup muffin pan
Ingredients
- 1 ¾ cups almond flour
- 1 cup tapioca flour (also called tapioca starch)
- ¼ cup coconut flour
- ½ cup coconut sugar
- 1 tsp. baking soda
- ½ tsp. fine sea salt
- 2 tsp. pumpkin pie spice
- ½ tsp. ground cinnamon
- 3 eggs (room temperature)
- 1 cup pumpkin puree (not pumpkin pie mix)
- ½ cup non-dairy/unsweetened milk
- ¼ cup coconut oil, melted
- 1 tsp. pure vanilla extract
Instructions
- Preheat oven to 350F. Lightly grease, or add muffin liners, to a 12-cup muffin pan; set aside.
- In a large bowl, whisk together the almond flour, tapioca flour, coconut flour, coconut sugar, baking soda, salt, pumpkin spice, and cinnamon.
- Make a well in the center of the dry ingredients and add the remaining wet ingredients (eggs, pumpkin, milk, melted coconut oil, vanilla). Whisk the wet ingredients together, and then fully mix the wet ingredients in with the dry ingredients. Do not overmix batter.
- Using a large spring-loaded cookie scoop (¼ cup size), scoop batter evenly between each well of the muffin tin (using a cookie scoop helps with the round muffin top). If you don't have a cookie scoop, a spoon works fine (you'll use about ¼ cup batter for each muffin).
- Bake for 24-27 minutes, or until a toothpick entered in the center comes out clean.
- Allow to cool before removing from the pan. Enjoy!
Notes
- When you measure the almond flour, scoop the almond flour into the measuring cup and level off with a knife. Do not pack the flour, or you will end up with too much.
- For slightly larger muffins, make 10 muffins.
- These are best within 2 days or baking. To extend freshness, store in the fridge.



Luci says
Delicious! I added chopped walnuts to give an extra boost.
Sara says
Love the addition of chopped walnuts. So glad you enjoyed these and thanks for sharing!
Janessa says
Love these healthier pumpkin muffins! We've been having them for breakfast this week.
Sara says
I love having them for breakfast, too!
Nancy says
I love that these are refined sugar free and much healthier than store bought. Thanks
Sara says
So much healthier than store bought 🙂
Shadi Hasanzade says
Love addition of almond flour in this recipe! These pumpkin muffins would be perfect with a cup of coffee in the morning!
Aimee Mars says
These are delicious. I made a double batch and love to have a muffin with my morning coffee.
Jess says
Love that I can enjoy my favorite pumpkin muffins in a healthier way with this recipe!