These Gluten-Free, Healthy Pumpkin Cookies Are Everything I Want This Fall

These healthy pumpkin cookies are the soft, cozy fall treat that was missing from my pumpkin recipe collection. I’d already turned my pumpkin obsession into healthy pumpkin pie, pumpkin bread, and more, but somehow I still didn’t have a cookie! I wanted these to be soft and moist, with real pumpkin and warm spices, and of course, without refined sugar. Here’s why these gluten-free pumpkin cookies check all the boxes:
- All the fall flavor – With real pumpkin, cinnamon, and nutmeg, these cookies taste like everything fall should be.
- Soft, moist texture – I wanted a soft, tender cookie with lightly golden edges, so don’t expect crisp and snappy here. These have a tender feel and vanilla frosting similar to my healthy pumpkin bars, but in cookie form.
- No refined sugar or wheat flour – I use Besti for natural sweetness and superfine almond flour for a delicate crumb. So not only are these gluten-free pumpkin cookies, they also have 4 grams of protein, 1.5 grams of fiber, and less than 1 gram of sugar each.
I love these pumpkin cookies with a glass of almond milk or a hot cup of coffee when I’m craving a cozy fall treat. Make a batch with me!


“I made these today and OMG! They are so good! I will make these all year long, not just in fall. Now I have 3 favorite cookie recipes.”
-Jeannette
Ingredients & Substitutions
Here I explain the best ingredients for my healthy pumpkin cookies, what each one does, and substitution options. For measurements, see the recipe card.
- Pumpkin Puree – Make sure you grab plain canned pumpkin puree like this, not pumpkin pie filling, which already contains sweetener and spices. Canned is my preference for the most consistent texture, but if you want to use fresh roasted pumpkin, you can. Just puree it until completely smooth and drain off any excess moisture.
- Wholesome Yum Blanched Almond Flour – This superfine grind is important here for your pumpkin cookies to turn out moist and tender instead of gritty or crumbly. Don’t substitute coconut flour, because it absorbs much more moisture and makes this recipe dry. Sunflower seed flour or macadamia nut flour are the closest alternatives, but the flavor and color can differ.
- Besti Powdered Monk Fruit Allulose Blend – I use this in both the cookies and glaze. It keeps the cookies moist without refined sugar, and the powdered texture dissolves smoothly. I don’t recommend most brands of monk fruit, stevia, or erythritol here, because they’ll leave the glaze gritty, even if they’re powdered. Liquid sweeteners (like maple syrup) are too runny, so won’t work either. You can use plain confectioners’ allulose, though, but increase the amount to 1/2 cup in the cookie dough.
- Unsalted Butter – Let it soften so it creams smoothly. For a dairy-free option, my favorite is butter-flavored coconut oil.
- Egg – You only need one, so a flax egg works just fine as an alternative.
- Cinnamon & Nutmeg – These give the pumpkin cookies their warm, cozy flavor. If you want ginger and clove notes or a stronger flavor, see my variation on that below.
- Heavy Cream – I mix this with powdered Besti to create a creamy, spreadable glaze. (For those of you who said the glaze was too runny, I adjusted the amounts recently to improve this!) Canned coconut cream works as a dairy-free substitute.
- Baking Powder (for lift — I like this non-GMO one!), Vanilla Extract, & Sea Salt (to balance the sweetness)
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How To Make Healthy Pumpkin Cookies
I have step-by-step photos here to help you visualize the recipe. For full instructions with amounts and temperatures, see the recipe card.
- Cream the butter and powdered Besti. In a large bowl, use a hand mixer to beat them together until fluffy.
- Add the other wet ingredients. Beat in the pumpkin puree, egg, and vanilla.
- Add the dry ingredients. This includes almond flour, cinnamon, nutmeg, baking powder, and salt. I stop mixing as soon as the dough is evenly orange with no dry pockets.


- Scoop and shape the cookies. Pack the dough into a medium cookie scoop, release it onto the lined baking sheet, and flatten each mound to about 1/4 inch thick.
- Bake in the oven, then cool. They’re done when the edges are light golden but the centers still look soft. Let the cookies cool completely on the pan before moving them.
- Glaze the cookies. Whisk the powdered Besti, heavy cream, and vanilla until smooth and spreadable, adjusting with a little more cream or sweetener if needed. Once your healthy pumpkin cookies are fully cooled, spread the glaze over them. I like an extra dusting of cinnamon on top!



My Recipe Tips
- Softened butter is key to creaming properly. If you forget to take it out of the fridge, don’t melt it. Instead, fill a metal bowl with boiling water to heat it up. Empty the water, dry, and place the bowl upside down over the sliced butter on a plate. The heat will soften the butter in a few minutes. Sometimes I have to repeat the process.
- This healthy pumpkin cookie dough is supposed to be very soft. This is normal! I don’t recommend adding extra flour.
- How to deal with sticky dough: Sometimes this dough works perfectly for me and other times it can stick to the scoop. If this happens, I find it helps to spray the scoop with oil (I love this glass spray bottle!). If that doesn’t help enough, you can chill the dough for 15-30 minutes in the fridge and try again. Wet or lightly oiled hands also help when flattening.
- Pumpkin cookie dough doesn’t spread much, so I flatten the scoops before baking. That gives you control over the final thickness.
- Don’t move them while they’re warm. These gluten-free pumpkin cookies are fragile coming out of the oven and can fall apart. They’ll firm up as they cool. Plus, the texture of the crumb inside will set in the process.
- You may need to adjust the amount of powdered Besti in the glaze to get it thick. It depends on how the powder settles, so a runny glaze just means you need more Besti. If you want it totally firm, I recommend refrigerating the cookies to help it set.

Healthy Pumpkin Cookies
My gluten-free, healthy pumpkin cookies have real pumpkin, fall spices, and creamy vanilla glaze. 4 grams of protein and no refined sugar!
Ingredients
[ See substitutions ]Tap underlined ingredients to see the ones I use.
Pumpkin Cookies:
Vanilla Glaze:
Instructions
[ See step photos See my tips ]Tap on the times in the instructions to start a kitchen timer.
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Preheat the oven to 350 degrees F (176 degrees C). Line a large baking sheet with parchment paper.
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In a large deep bowl, beat together the butter and Besti, until fluffy.
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Beat in the pumpkin puree, egg, and vanilla.
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Beat in the almond flour, cinnamon, nutmeg, baking powder, and sea salt, until a uniform cookie dough forms.
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Use a medium cookie scoop to scoop balls of dough and pack the dough into it. Release onto the lined baking sheet, 2 inches (5.08 cm) apart. Use your palm, or the bottom of a glass with a twisting motion, to flatten cookies to about 1/4 inch (.64 cm) thick.
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Bake for 12 to 15 minutes, until light golden on the edges. Cool completely to firm up before moving from the pan.
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Meanwhile, make the glaze/frosting, if using. In a small bowl, whisk together the glaze ingredients until smooth: heavy cream, powdered Besti, and vanilla. If it's too thick, add more cream, a teaspoon at a time, until it's a spreadable consistency. If it's too thin, add more powdered Besti to thicken.
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Spread a teaspoon of glaze on top of each pumpkin cookie (or simply sprinkle with powdered Besti instead).
Did you make it? Leave a review or tag me @wholesomeyum on Instagram!
Maya’s Recipe Notes
Serving size: 1 healthy pumpkin cookie (2″ diameter)
- Tips: Check out my recipe tips above to help you deal with the dough if it’s sticky, get the right consistency, prevent the cookies from falling apart, and more.
- Storage: Keep these healthy pumpkin cookies in an airtight container for up to 5-7 days. I refrigerate them if I add the cream glaze.
- Freeze: Freeze completely cooled cookies in a single layer, or between sheets of parchment paper, for up to 2-3 months. You can freeze them with or without the glaze, or even freeze the raw cookie dough. Thaw at room temperature before serving.
I provide nutrition facts as a courtesy. Have questions about calculations or why you got a different result? Please see my nutrition policy.
Add Your Notes Your Notes
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Healthy Pumpkin Cookies
Recipe Variations
I like these healthy pumpkin cookies just the way they are, but I’ve also experimented with a few different spins on them. Try these if you want to add a little something or change the texture:
- Extra pumpkin spice – These cookies have a subtle spice thing going, not dramatic. For a bolder pumpkin spice flavor, replace the cinnamon and nutmeg with 1 tablespoon of pumpkin pie spice plus another 1/2 teaspoon of cinnamon.
- Add-ins – Fold 1/4 to 1/2 cup of chocolate chips (I like these sugar-free ones for pumpkin chocolate chip cookies) or chopped nuts (like walnuts or pecans) into the cookie dough.
- Chewier – These gluten-free pumpkin cookies are naturally soft and tender. If you like a chewy bite, sprinkle 1/4 to 1/2 teaspoon of xanthan gum into the dough. The best time to add it is together with the almond flour and spices.
- Swap the glaze – I highly recommend something on top because these cookies are only lightly sweet on their own! If you don’t want the vanilla cream glaze, you can use my tangy cream cheese frosting, drizzle or dip in melted chocolate, or just dust the pumpkin cookies with powdered Besti.

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86 Comments
Christina
0These cookies are incredible! I love anything pumpkin and these are so easy to make!
Katie
0Yes! Just in time for fall! These don’t disappoint.
Lori
0Hi Maya! I made these today and they turned out perfect! I used 1 tsp nutmeg but noticed it isn’t mentioned in the ingredients list of how much to use. Thank you for all of you wonderful recipes, everything I have tried has been delicious.
Steve
0These sound really good! Could I use coconut flour instead of almond flour? I have a nut allergy.
Wholesome Yum M
0Hi Steve, I’m sorry that won’t work in this recipe.
Robyn
0Hi! Where do we add the xanthan gum if we are using it? Thanks!
Wholesome Yum M
0Hi Robyn, Xanthan gum can go in at the same time with the almond flour and spices.
Amy Molitor
0I don’t see a measurement for the nutmeg?
Wholesome Yum M
0Hi Amy, It’s 1/2 tsp of nutmeg 😉
Kristen Wood
0These look perfectly delicious!!
Wholesome Yum A
0Could I sub full fat coconut milk instead of cream?
Wholesome Yum M
0Hi Amanda, Yes but be sure to separate the coconut cream from the coconut water in the can. Place it in the fridge for a couple of hours. When you open it scoop out the coconut cream solids and discard (or save) the coconut water. Use the cream to make your frosting. Enjoy!
Lily
0I just started keto and these recipes have been a lifesaver!
Betty
0I followed the keto pumpkin cookies recipe, icing is great but cookies taste more like eating almonds cookies than tasting like pumpkin cookies. Thanks for posting recipe thou..