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Home Recipes Desserts Breads & Muffins
4.9 from 10 reviews

Moist & Fluffy Pumpkin Cream Cheese Swirl Muffins with almond flour

40 min
GF Gluten-Free VG Vegetarian
by: Lindsay Grimes
August 25, 2020 (Updated: September 6, 2023)
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overhead image of three pumpkin cream cheese swirl muffins one with its muffin wrapper unwrapped sitting on a white counter
Gluten Free Pumpkin Muffins have a delicious cream cheese swirl! They are fluffy, moist, and made with almond flour!

The unofficial start of pumpkin season is only a few weeks away. To be honest, I don’t know the exact date that unofficial start is, but there’s always a moment in September where I think to myself, “It’s time…”

Since I want to prep you for when that day comes. For when that pumpkin bell rings… I’m starting now.

Sure sure, you can say it’s premature. Me? I say it’s planning for the future.

overhead image of four pumpkin cream cheese swirl muffins, one laying on it's side with a bite taken out

These pumpkin swirl muffins are:

  • fluffy
  • moist
  • warm cream cheese pool in the middle
  • pumpkiny but not overwhelmingly pumpkiny
  • perfect any time of day
  • super simple to make
overhead image of all the ingredients to make pumpkin cream cheese swirl muffins

Gluten Free Pumpkin Muffin Ingredients:

  • pumpkin puree: I used canned pumpkin puree, but here’s my tutorial on how to make your own pumpkin puree!
  • eggs: I haven’t tested it with flax eggs, so if you give it a try, let me know how it goes!
  • coconut sugar: if you don’t have coconut sugar, brown sugar or another granular sugar may be a good sub!
  • vanilla extract
  • blanched almond flour: I love blanched because it’s super fine and light. But, it’s not essential to the recipe. If you’re ok with a heartier texture, unblanched or almond meal could probably work too.
  • arrowroot flour: this adds such a lightness and fluffiness to the recipe. Arrowroot flour, arrowroot starch and arrowroot powder are all the same thing 🙂
  • pumpkin pie spice: a beautiful blend of autumn spices that I buy in a container pre-made.
  • ground cinnamon
  • baking soda
  • baking powder
  • salt

Cream Cheese Swirl:

  • cream cheese: I haven’t tested it with a dairy free cream cheese, but if you want to keep this recipe completely dairy free, I think it would be fun to experiment with it!
  • agave nectar: honey or maple syrup would also be a good sub!
  • vanilla extract

How to make Gluten Free Pumpkin Muffins:

Use a handheld electric mixer to cream together the pumpkin, eggs, coconut sugar and vanilla in a large bowl.

Add the almond flour, arrowroot flour, pumpkin pie spice, baking soda, baking powder, cinnamon, and salt to the bowl. Mix again until combined.

Scoop the batter into a muffin pan lined with parchment paper muffin liners. I love using an ice cream scooper to make sure all the muffins are filled the same amount. Set aside.

In a medium bowl, cream together the cream cheese, agave nectar, and vanilla with an electric mixer. Once soft, scoop 1 tablespoon onto each muffin. I like to create a divot at the top of each muffin to create a little pool in the center that goes down into the center top of the muffin.

Once all the muffins have cream cheese on them, use a chopstick or toothpick to swirl it onto the top of the muffin.

Bake for 25 minutes until the tops are puffed up and set. Remove from the oven to cool. The center where the cream pool was may dip down a bit. I kinda like it but just want to warn you to not be upset if the centers do drop a bit as they cool.

Store in an airtight container in your fridge!

side view of a pumpkin cream cheese muffin with a bite taken out

Did you make this? Leave a review below and tag me on Instagram, Facebook, or Pinterest!

Recipe
GF Gluten-Free VG Vegetarian

Moist & Fluffy Pumpkin Cream Cheese Swirl Muffins with almond flour

These Pumpkin Cream Cheese Swirl Muffins are fluffy, moist, and naturally gluten free made with almond flour! Such a delicious fall treat!

Recipe by:Lindsay Grimes
5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.9 from 10 reviews
Prep: 15 minCook: 25 minTotal: 40 min
Print recipe Rate recipe Pin Save recipe
Servings: 12 muffins

Ingredients

Pumpkin Muffins:

  • 1 cup canned pumpkin puree
  • 3 eggs
  • 1/2 cup coconut sugar
  • 1 teaspoon vanilla extract
  • 1 cup blanched almond flour
  • 1/2 cup arrowroot flour
  • 2 teaspoons pumpkin pie spice
  • 1/2 teaspoon ground cinnamon
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/2 teaspoon salt

Cream Cheese Swirl:

  • 4 oz cream cheese, room temp or warmed in the microwave for 30 seconds
  • 2 tablespoons agave nectar
  • 1/2 teaspoon vanilla extract

Instructions

  1. Preheat oven to 350F.
  2. Use a handheld electric mixer to cream together the pumpkin, eggs, coconut sugar and vanilla in a large bowl.
  3. Add the almond flour, arrowroot flour, pumpkin pie spice, cinnamon, baking soda, baking powder, and salt to the bowl. Mix again until combined.
  4. Scoop the batter into a muffin pan lined with parchment paper muffin liners. I love using an ice cream scooper to make sure all the muffins are filled the same amount. Set aside.
  5. In a medium bowl, cream together the warm cream cheese, agave nectar, and vanilla with an electric mixer.
  6. Once soft, scoop 1 tablespoon onto each muffin. I like to create a divot at the top of each muffin to create a little pool in the center that goes down into the center top of the muffin.
  7. Once all the muffins have cream cheese on them, use a chopstick or toothpick to swirl it onto the top of the muffin.

  8. Bake for 25 minutes until the tops are puffed up and set.
  9. Remove from the oven and set aside to cool in the pan for 10 minutes. The center where the cream cheese pool was may dip down a bit as they cool.

Nutrition Info:

  • Serving Size: 1 muffin
  • Calories: 116
  • Sugar: 11.4g
  • Sodium: 214mg
  • Fat: 5.6g
  • Saturated Fat: 2.6g
  • Unsaturated Fat: 0g
  • Trans Fat: 0g
  • Carbohydrates: 14.3g
  • Fiber: 1.2g
  • Protein: 3g
  • Cholesterol: 51mg
© The Toasted Pine Nut

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  1. AvatarAimee Duncan says

    Posted on 11/12/20 at 1:20 pm

    These are amazing! Just wanted to ask, how do you prevent them from sticking to the muffin lining when done? Any hacks or am I missing a step?

    Reply
    • Lindsay Grimes Freedman says

      Posted on 11/13/20 at 8:08 am

      Hm, do you use parchment paper liners? They usually work for me. You could also give them a little spray to make sure they don’t stick. I’m glad you enjoyed them!! xo

      Reply
  2. AvatarKatie says

    Posted on 11/16/20 at 2:49 pm

    I’ve been eyeing these and finally made them and SO GLAD I DID. These are fantastic. I love how quick they were to mix up and are the perfect Fall muffin (that tastes like pumpkin pie) 

    Reply
    • Lindsay Grimes Freedman says

      Posted on 11/16/20 at 8:05 pm

      Yay! I’m so glad you loved them!! xo

      Reply
  3. Hannah says

    Posted on 11/23/20 at 10:12 pm

    Oh man. Just made these and they were amazing!!! Substituted cornstarch for arrowroot flour because I was out. Then used a pumpkin cashew cream (similar to the filling for the pumpkin cheesecake bars in an earlier recipe). Added a drizzle of honey and pecans on top and it was so so good. Definitely will be making again.

    Reply
    • Lindsay Grimes Freedman says

      Posted on 11/30/20 at 11:00 am

      Ah that sounds amazing!! I’m so happy you enjoyed!! xo

      Reply
  4. AvatarKaren says

    Posted on 11/1/21 at 10:36 am

    WOW!!! Made these on the weekend , and OH EM GEE . Probably the best muffin i’ve ever made. They, by no means, taste gluten free, or refined sugar free or only just over 100 calories . An absolute keeper of a recipe!

    Reply
  5. AvatarValarie says

    Posted on 11/17/21 at 8:55 am

    This recipe is delicious !

    Reply
    • Lindsay Grimes Freedman says

      Posted on 11/22/21 at 9:01 am

      Thank you!! They’re one of my faves this time of year! xo

      Reply
Older Comments

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Lindsay

Nice to Meet You!

I’m Lindsay - cookbook author, blogger and chocolate lover! If gluten-free desserts are your jam, you’re in the right place! I live in south Jersey with my family and new puppy Roxie! Some of my favorite things are oat milk lattes, sunny days and warm, gooey chocolate chip cookies.

Read more...

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GF Gluten-Free DF Dairy-Free V Vegan VG Vegetarian EF Egg-Free NF Nut-Free P Paleo Browse All

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