These delicious almond flour pumpkin muffins say "fall" with every bite! They're moist and soft with a cream cheese swirled top and loads of pumpkin flavor. Naturally gluten free and can easily be made dairy free too!
Calling all fall fans!! The best time of year has arrived and these pumpkin muffins have your name written all over them. They're packed with cinnamon-y pumpkin spice flavor and a cream cheese-style top. It's like pumpkin muffin meets pumpkin cheesecake!
Made with almond flour, these muffins are gluten free and can be made dairy free with a simple swap so everyone can take part in the fall fun!
You will also love my mini pumpkin pies and my pumpkin cinnamon rolls for more pumpkin recipes!
Ingredients and Substitutions
- Eggs - Use room temperature large eggs for this recipe. The eggs help to bind the batter together and ensure the muffins rise well in the oven. I have not tried this recipe with an egg replacer so I can't recommend one.
- Pumpkin - This is pure pumpkin puree, not pumpkin pie filling. You can find it in the baking aisle at the grocery store and should come in a can and the only ingredient will be pumpkin.
- Almond butter - Any type of nut or seed butter will work. This is the fat source used in these healthy pumpkin muffins and helps create a soft and moist texture.
- Coconut sugar - Used to sweeten the muffins. You can also use brown sugar if desired.
- Apple cider vinegar - This is important and no, you won't taste it. In gluten free baking, there usually needs to be an "acid" ingredient to help activate the leavening agent so the batter will rise in the oven. I like to use apple cider vinegar because I have it on hand but you can also use lemon juice.
- Almond flour - The main flour used in the muffins to make them gluten free. Almond flour is naturally soft which is perfect for moist pumpkin muffins!
- Tapioca flour - The combination of almond flour and tapioca is best for super fluffy muffins. The tapioca flour helps to cut the density from the almond flour. You can also use arrowroot starch.
- Pumpkin spice - What is a pumpkin muffin without pumpkin pie spice?? A generous 1 teaspoon is used in the muffin batter. If you don't have pumpkin spice mix, you can use a little cinnamon, nutmeg, cloves, and ginger.
- Cream cheese - Used to make the cream cheese batter that is swirled into each muffin. Make sure it's soft and at room temperature. If dairy free, use a vegan cream cheese.
- Egg yolk - Mixed into the cream cheese mixture to help it form a cheesecake like texture and flavor in the oven.
How to Make Almond Flour Pumpkin Muffins
You will need a mixing bowl with an electric mixer, stand mixer, or stiff whisk and a muffin tin with liners.
Step 1 : Mix together the wet ingredients. Add the eggs, vanilla extract, pumpkin, almond butter, coconut sugar, and apple cider vinegar to a large bowl. Mix well with a mixer or stiff whisk until the pumpkin and almond butter are well incorporated. The batter will be orange and slightly thick.
Step 2 : Fold in the dry ingredients. Add the almond flour, tapioca starch, pumpkin spice, baking soda, baking powder, and sea salt to the bowl and gently fold with a rubber spatula until no flour clumps remain.
Step 3 : Make the cream cheese mixture. In a separate medium bowl, beat together the softened cream cheese with the egg yolk and sugar until smooth and creamy. This is best done with a hand or stand mixer.
Step 4 : Assemble the muffins. Use a large cookie scoop to scoop the muffin batter into a muffin pan with paper liners. Fill the liners up ¾ of the way full. Then use a ½ tablespoon spoon to place dollops of the cream cheese mixture on top of each muffin. Swirl the cream cheese into the tops of the muffin batter with a toothpick or a thin knife.
Step 5 : Bake! Transfer the muffin pan to the preheated oven to bake until the muffins have risen and the cream cheese on top has set. The cream cheese will look puffy and domed but will settle a little as it cools down.
Let the muffins cool for no more than 5 minutes in the pan before transferring the muffins to a wire rack to cool completely. This will prevent wet and soggy muffins which is super important when you're baking with pumpkin.
Once the muffins have cooled, sprinkle a little coarse cane sugar on top if desired and enjoy!
How to Store
Place the cooled muffins in an air-tight container. Use some parchment paper in between layers so the muffins don't stick together if you stack them on top of one another.
Store the sealed container out on the counter for up to 4 days or in the fridge for up to a week (my preferred method). You can also freeze the muffins in a freezer bag or airtight container for up to 3 months. Simply thaw the muffins out on the counter or in the fridge until soft.
- Make sure to mix the pumpkin and almond butter well into the wet ingredients. You don't want chunks of pumpkin or almond butter in the muffins.
- Don't be afraid to fill up the muffin liners more than you normally would. Because these are gluten free muffins, they won't rise as much as traditional muffins.
- As soon as you can handle the muffins with your hands, remove them from the muffin tin and onto a cooling rack. This is key in preventing the bottoms of the muffins from getting too soft and wet. The condensation from the muffins cooling down will leak into the muffins if you're not careful.
Can I make these muffins without the cream cheese?
Yes, the cream cheese swirl is to add some more flavor to the muffins and make them a little more elevated. You can use a variety of mix-ins though instead of the cream cheese. Here are a few easy ways to mix things up:
- Chocolate chips
- Chopped pecans
- White chocolate chips
- Pumpkin seeds
- Add some cinnamon sugar in the middle of each muffin by filling up the liners half way, sprinkling some cinnamon sugar and then adding more batter on top.
- Make an easy streusel to go on top of the muffins. You can use the streusel in my gluten free coffee cake.
Frequently Asked Questions
This can happen if you let them cool all the way in the muffin pan. Remember to transfer them to a cooling rack once they are warm enough to handle with your hands. Because almond flour is so soft, it can also become soggy if too much wet ingredients are used. This is why we use almond butter as the fat source instead of vegetable or coconut oil.
They are pretty much the same. The only difference is that almond meal is made from unpeeled almonds so you will see little specks of brown in the flour from the skins of the almonds.
Check out these recipes for more pumpkin fun!
PS : If you make this recipe, be sure to leave a star review and comment below! Also be sure to follow along with me on Instagram and Pinterest to stay up to date on all tasty recipes here at The Fit Peach!
Almond Flour Pumpkin Muffins
- 2 eggs
- 1 teaspoon vanilla extract
- 1 cup pumpkin puree
- ¼ cup almond butter
- ⅔ cup coconut sugar
- 1 tablespoon apple cider vinegar
- 2 cups almond flour
- ¼ cup tapioca flour
- 1 teaspoon baking soda
- ½ teaspoon baking powder
For the cream cheese swirl
- 5 oz cream cheese - softened and at room temperature
- 3 tablespoon sugar
- 1 egg yolk - at room temperature
- Preheat oven to 375 F. In a large bowl, mix together the eggs, vanilla, pumpkin puree, almond butter, coconut sugar, and apple cider vinegar until well combined with a hand or stand mixer or stiff whisk.
- Fold in the almond flour, tapioca flour, baking powder, and baking soda until no flour clumps remain. Set the bowl aside.
- In a separate bowl, beat the cream cheese with the sugar and egg yolk until smooth and creamy.
- Line a muffin pan with liners and scoop the muffin batter into each liner, filling it about ¾ of the way full. Use a ½ tablespoon to place a dollop of the cream cheese filling on top of each muffin. Then use a toothpick or thin knife to swirl the cream cheese into the muffin batter. This doesn’t need to be perfect. Simply swirl to distribute the cream cheese to the edges of the muffin and down into the middle.
- Bake the muffins in the oven for 15 - 18 minutes until they have risen and the cream cheese on top has turned a beige color and looks set. Let the muffins cool slightly for no more than 5 minutes before transferring them to a cooling rack. This is important! Don’t leave the muffins in the hot pan for too long or you will end up with soggy and wet muffin bottoms. Sprinkle a little coarse cane sugar on top of the muffins if desired and enjoy!
In the ingredient list when I printed the recipe it doesn’t mention pumpkin spice but it lists it as an ingredient at the top of the article.
I don’t have tapioca flour. Will the recipe still work or is there any other flour I can substitute like coconut flour?
Adamelis Orozco says
Muchas gracias por la receta me encantó 🥰👏👏
Diane Cravedi says
Super easy and very very yummy! I love that they aren’t super sweat or have the pumpkin pie spices although you can certainly add them. I prefer without! Highly recommend these. I made them with Kite Hill dairy free cream cheese and honestly don’t feel like they taste any different 😁