Gluten Free Oatmeal Chocolate Chip Pumpkin Cookie Recipe

Last Updated on September 22, 2026 by The Allergy Chef

It’s Fall (I think) and that means it’s time to break out the pumpkin! I hope you’re ready to make some darn good chocolate chip pumpkin cookies, because these bad boys are loaded with pumpkin flavor, warm spices, and are like that cozy little treat you want after a long day at work. Or in your lunch box.

These gluten-free pumpkin chocolate chip cookies also double as an oatmeal cookie. If that’s not your jam, let me point you towards these epic gluten free vegan pumpkin snickerdoodle cookies instead.

Either way, know that this fall season, you won’t find awesome gluten free cookies like this at the grocery store, so grab your ingredients and let’s get to work.

Table of Contents

Allergy Status

Free From: Wheat/Gluten, Dairy, Egg, Soy, Tree Nuts, Peanut, Fish, Shellfish, Sesame, Top 9 Allergens, Alliums, Apple, Avocado, Banana, Beans & Lentils, Berries, Buckwheat, Carrot, Celery, Cinnamon, Citrus, Coconut, Cruciferous, Garlic, Latex Cross Reactive Foods (H/M), Legume, Lupin, Mushroom, Mustard, Nightshades, Onion, Pea & Pea Protein, Potato (Nightshade Variety), Poultry, Red Meat, Rice, Stone Fruits, Strawberry, Sweet Potato & Yam, Tapioca/Cassava/Yuca/Manioc, Tomato, Yeast

Friendly To: EOE, Vegan

Tools Needed for This Pumpkin Oatmeal Cookies Recipe

Kitchen Scale (this is the one that I love)
Small Bowl (for flax gel OR beating your eggs)
Stand Mixer with Paddle Attachment OR Handheld Electric Mixer + Large Bowl
Baking Tray
Parchment Paper (you won’t need cooking spray)
Spatula (this is the one that I really like)
Cookie Scoop (a medium cookie scoop is the ideal size for these delicious pumpkin cookies)

Ingredients for Your Gluten Free Pumpkin Cookies

Flax Gel/Bind

5 TBSP Golden Flax Meal (use this brand for the best results)
10 TBSP Water (room temperature)

Note: sometimes this is called a flax egg, but I don’t use the term since there isn’t a universal measurement.

Part 1 Ingredients (Wet Ingredients)

225g Dairy Free Butter (also called vegan butter) OR Unsalted Butter
200g Organic Dark Brown Sugar
100g Organic White Sugar (also called cane sugar)

Part 2 Ingredients (Dry Ingredients)

OK, dry ingredients, plus vanilla.

420g Organic Pumpkin Purée (15 ounces, this is the one that I use)
300g Organic Gluten Free Purity Protocol Rolled Oats
160g Chocolate Chips of Choice (mini chocolate chips suggested, you can use dark chocolate chips, white chocolate chips, etc.)
100g Organic Gluten Free Purity Protocol Oat Flour
85g Sorghum Flour, superfine OR Brown Rice Flour, superfine
4 tsp Baking Powder
3 tsp Organic Vanilla Extract
1.5 tsp Sea Salt

Ingredient Notes & Substitutes

Flax + Water: If you’re not vegan or allergic to eggs, you can use 2 large eggs in place of the flax/water combo. Place your eggs into a small bowl and whisk them very well. Where the instructions call for the flax gel, pour in your whisked large eggs.

Dairy Free Butter: Do not swap this for a fat that’s liquid at room temperature (olive oil, vegetable oil, sunflower oil, etc.). You can swap this for a fat that’s solid at room temperature such as palm shortening. However, any change to the vegan butter will cause an absolute shift in the taste and texture of these gluten free pumpkin cookies.

Dark Brown Sugar: In a pinch, you can swap this for organic light brown sugar, but you will lose some of the molasses content, and that little bit of extra depth in the flavour of these delicious cookies.

Organic White Cane Sugar: This is another granulated sweetener and you can swap it for organic maple sugar to slightly alter the taste of your gluten free pumpkin cookies, but also to reduce the overall sweetness of the cookies as well. Liquid sweetener substitutions will not work (maple syrup, agave, etc.).

Gluten-Free Oat Flour & Gluten-Free Rolled Oats: If you don’t need organic and Purity Protocol, you can use regular oat flour and regular rolled oats.

Sorghum Flour: Of the gluten free flour in this pumpkin cookie recipe, only the sorghum can be swapped since it’s an oatmeal cookie. You can exchange this for a gluten free all purpose flour. Avoid gluten-free flours including cassava flour, coconut flour, almond flour, nut flours, seed flours, and starches (arrowroot, potato starch, etc.)

Canned Pumpkin Puree: This is an unsweetened product. Pumpkin pie mix on the other hand has a lot of sweetness from the added sugar, but also has the added bonus of the pumpkin spice blend already mixed in. You can use regular canned pumpkin puree, pumpkin pie mix, sweet potato puree, or butternut squash puree when making these tasty cookies.

Directions for These Gluten Free Pumpkin Cookies

Oven Temperature: 325f/163c
Bake Time: 16 – 18 Minutes
Cool on Tray Time: 15 Minutes

Before you grab ingredients for these easy gluten-free pumpkin cookies, preheat your oven to 325f/163c.

I’ll be using a stand mixer with the paddle attachment to make these awesome gluten free pumpkin cookies. If needed, you can use a large mixing bowl (I don’t suggest a medium bowl because you’ll make a mess as you mix and everything spills over the sides) with an electric hand mixer. You *could* mix by hand, but it’s going to require some elbow grease.

Start by lining a large baking tray with parchment paper and preheating your oven. Next, combine your flax and water together in a small bowl and set aside, allowing it to gel whilst you get everything else together.

Place your mixing bowl on your kitchen scale and tare to zero. Add the Part 1 Ingredients (butter and sugar). Once it’s in, cream (mix) your butter and sugars together on medium speed. When they’re well combined, turn the mixer off.

Scrape down the edges of the bowl, and place it back on your kitchen scale. Tare to zero, then add all of your other ingredients (don’t forget the flax gel, and don’t forget to tare between weighted ingredients).

Connect your bowl to the stand and mix again. Start on low speed and pulse the mixer off and on to prevent having a massive gluten free flour mess in your kitchen (and on your person). Once enough of the flour is wet, mix on medium-high speed until your cookie dough fully forms. Once it looks good, turn the mixer off.

Use a cookie dough scooper of any size to portion out your dough. Roll into balls, place on your prepared baking sheet, and press down slightly on your dough balls. I tested small, medium, large, and extra large cookies. There was no discernible difference in the sizes, but the kids preferred the larger cookies (because kids).

Bake at 325f/163c for 17 minutes, and allow your cookies to cool completely on the tray before serving.

More Awesome Gluten Free Cookie Recipes

Each of these gluten free cookie recipes is vegan, dairy-free, egg free, and so much more.

Soft Baked Gluten Free Sugar Cookies (these cookies have an amazing cake-like texture)
Gluten Free Lemon Cookies (you HAVE to make these if your a fan of softer cookies)
Gluten Free Snickerdoodle Cookies from my Bakery (some of the best gluten and dairy-free cookies you’ll ever eat)
Vegan Gluten Free Soft Baked Gingerbread Cookies (these soft cookies are BOMB, and blow away a traditional ginger snap, unless you’re like, all for the snap)

How to Store Your Gluten Free Pumpkin Cookies

After you’ve got amazing baked cookies, and now it’s time to store them (assuming you didn’t have a bunch of friends over and you guys were like, let’s just eat the whole batch). You can store your cooled cookies on the countertop at room temperature for 4 days (covered), or you can freeze them for many months (the best way if you ask me).

One of the best things about this recipe is that your cookies are freezer friendly. To freeze your cookies, place them on a single layer on your large baking tray. It’s OK if the sides are touching. If you need a second layer, place a piece of parchment paper over the first layer of pumpkin cookies first. The pieces of parchment paper between the layers will prevent the cookies from freezing together and clumping or being hard to separate.

Place the entire baking tray into your freezer. Once your cookies are frozen solid, transfer them to an airtight container or freezer bag. Be sure to label your freezer-safe container with the flavour and date.

These cookies can be frozen for 4 – 6 months before you start to see a decline in the texture. To thaw, leave some cookies out on the counter, at room temperature for 45 – 60 minutes. Once thawed, you’ve got the perfect little treat.

How to Tweak This Gluten Free Pumpkin Cookie Recipe

OK, Let’s take a look at a few delicious ways you can alter this gluten free pumpkin cookie recipe:

Swap the pumpkin puree for pumpkin pie filling. Keep in mind though, if you do this, your gluten free pumpkin cokes are going to be much sweeter since canned pumpkin filling is a sweetened product.
Top with a pumpkin pie spice glaze (here’s a great pumpkin spice recipe if you need one).
Top with Organic Maple Butter (this is a dairy free product that’s whipped maple syrup and comes in a glass jar, but some grocery stores now sell literal butter + maple in the produce section)
Top with cream cheese frosting (here’s a recipe for Dairy Free, Vegan Cream Cheese Frosting).
For fun, make baby cookies! Portion out tablespoon-sized dough balls or use a small cookie dough scoop your smaller cookies can be used for the cutest mini ice cream sandwiches (pair with vanilla, cinnamon, or pumpkin ice cream) ok, or chocolate ice cream if that’s your jam.
Bake your cookies a little longer so they get crispy, then break them up and use like a granola topping for yogurt on the weekend.

More Delicious Pumpkin Desserts

If you’re putting together a holiday table, or a dessert table that’s an ode to pumpkin, in addition to this awesome gluten-free pumpkin cookies recipe, try making these as well:

Easy Gluten Free Pumpkin Waffles Recipe (serve with a chocolate dip, or with ice cream, and it’s a dessert)
Easy Eggless Baked Pumpkin Donuts Recipe (I’m told these are over the moon delicious)
Awesome Vegan Pumpkin Snickerdoodle Cookie Recipe (make these if you like soft pumpkin cookies with crisp edges)
Moist Gluten + Egg Free Pumpkin Bread Recipe (top with this dairy free cream cheese frosting for a proper dessert experience)

Answering Your Questions About This Gluten Free Pumpkin Cookie Recipe

Can I use coconut sugar in place of the white sugar and brown sugar?

If you swap all of the sugar for coconut sugar, you may be a little disappointed with your pumpkin cookies in the end. The sugars work together in terms of their molasses content to create a lovely balanced flavour.

You won’t get that from coconut sugar, date sugar, or maple sugar. Now, if you were to only trade one of the sugars, you’ll have better results. In terms of function though, yes, you can make that swap and still have gluten free pumpkin cookies that WORK. They’re just going to taste very different compared to the recipe that I’ve shared, so proceed with caution (and maybe start with a half batch).

Could I use coconut oil instead of dairy-free butter?

This is a “just because you can doesn’t mean you should” situation. Well, for most people. Coconut oil has a TASTE and if you don’t love it so much that you want to marry it, don’t make this swap. Seriously, you need to LOVE coconut. Like, open a joint bank account together and everything kind of love.

If you don’t love the taste of coconut oil that much, and you can’t use dairy-free butter, you can use palm shortening or avocado shortening in its place. They will alter the taste and texture a bit, but you’ll still have a pretty good cookie in the end.

Will this make an edible pumpkin cookie dough?

Yes and no. So, a lot of people think that the whole egg in most cookie recipes is the reason you can’t eat it raw. It’s also the flour. In the case of these egg free pumpkin cookies, there’s an easy trick to make it an edible dough: roast/bake the flour. Here’s how it works.

Measure out the flour, including the rolled oats.
Transfer the flour to a large baking tray covered in parchment paper.
Oven roast at 350f/175c for 20 minutes, or until you see some golden brown development. It’s important to spread the flour evenly so you don’t have a bunch of burned little bits in the corner of the tray.
Allow the flour to cool completely (don’t get impatient and skip this step).
Make this pumpkin cookie recipe as instructed. When it’s time to add the flour, add your cooled roasted flour.
When the cookie dough is done, now you have a proper, safe, edible cookie dough.

Since this recipe contains pumpkin, you’ll need to store your edible cookie dough in the fridge. It’s OK to leave it out for 30 minutes if you don’t want it to “taste cold”. You can also pre-portion your edible cookie dough and freeze it. This allows you to grab a little container in the future and have a nice fall treat.

Can I use just one teaspoon vanilla extract?

If you’ve run out, I’ll allow it. If you have a tolerance threshold you can’t cross, I’ll totally allow it. If you have a bunch of vanilla extract in your pantry and are just reducing to mess about, I’ll tell you now, your cookies will taste better with more vanilla extract.

However, know that reducing the vanilla won’t impact anything major. The pumpkin flavor will still be there, you’ll have that classic oatmeal chewy texture, and so on. Just, with lest pop from the vanilla.

What exactly is pumpkin pie spice?

This is a great question. So, pumpkin pie spice is a mix of ground cinnamon and other warm spices including allspice, nutmeg, and sometimes ginger. Whilst there aren’t any hard and fast rules on what has to be in your pumpkin pie spice, or the ratios, it’s usually heavy with ground cinnamon. From there, the other warm spices play a supporting role.

Also, if you want to make this at home, and opt to include cloves, only use a small amount (a little bit goes a long way). I’ve also got this great recipe for pumpkin pie spice if you’d like to give it a go.

Would these cookies taste good with crushed nuts?

Maybe. I think to add crushed nuts to this pumpkin cookie recipe, you’ll want to do a 50/50 mix of chocolate chips and crushed nuts. Also, pick a nut that’s going to really compliment the pumpkin. If I had to pick, I’d use cashews, almonds, or pecans.

What’s the best 1-to-1 gluten-free flour to use?

So, you need some context first. I am allergic to more than 200 items and have contact and airborne reactions. I’m deathly allergic to corn, and corn derivatives are in most products you can purchase in a grocery store. What that means is: I don’t experiment with most commercial items. Instead, I purchase safe raw materials in bulk to develop free-from recipes (that I can’t even eat).

So, I can only go on what my recipe developer friends have told me, and what I’ve seen online. Now that you know that, here’s my take.

The best all purpose gluten-free flour blend might be from a company called Better Batter. They’re not very well known, but they’ve crafted a different flour blend that you don’t see every day. Their development chef is a really cool dude, and he shows me what their different blends can do, and it’s IMPRESSIVE. It’s also gum free, making it even better to someone with my personal bias.

From there, I’ve heard so many great things about the King Arthur Measure for Measure Flour. Like, people rave about that stuff online, so it might be really, really good. I hear grain free people saying relatively good things about Pamela’s flour blend.

Interestingly, Bob’s Red Mill seems to always come up last, but they have the biggest shelf space and that could be because of the price point. But, remember the old saying, you get what you pay for? It could be a matter of that.

If I weren’t allergic to everything, I’d purchase every gluten free flour blend on the market and do a head to head bake WITH blind tastings from people who aren’t gluten free (but have great palates). Ultimately, if they give it the green light, you know it’s really good because they know what the alternatives are.

So, all of that to really say, I can’t tell you. You should do a side by side test bake, and then decide what YOU like best. Happy baking!

Do I need to chill these cookies before baking?

Great news! No, you don’t need to chill this pumpkin cookie dough in the fridge before baking. Just follow the tasty recipe and pop your cookies straight into the oven once your tray is loaded.

Should I cool these vegan cookies on a wire rack?

No, you don’t need to cool these gluten free vegan cookies on a cooling rack. Just allow them to cool on the baking tray for 10 to 15 minutes after they come out of the oven as directed, and you’ll be good to go. Happy baking!

Could I use Bob’s Red Mill all purpose gluten-free flour in place of your flour?

Generally, you can swap my gluten-free flour blend for something like Bob’s Red Mill All Purpose Gluten-Free Flour (or King Arthur Measure for Measure Flour that’s GF). However, there will be some differences since it is a different blend and usually contains extra ingredients like xanthan gum.

If you opt to swap, just make sure you manage your expectations and go into it eyes wide open because not all GF flours are created equally, and I make a custom free-from blend for each recipe that I develop.

Are old fashioned oats the same thing as rolled oats?

Yes, they’re going to be the same thing. And in case you need to know, gluten free oats are a 1:1 swap for old-fashioned oats. Also, steel cut oats are not the same thing and should not be used as a substitute.

Can I use baking soda instead of baking powder?

Nope, and I’m so glad you asked because they aren’t the same thing. Well, no as a 1:1. Generally, you don’t want to use more than half a teaspoon of baking soda in a batch of cookies. If you use more, you’ll negatively impact the flavour. Some recipes can get away with up to a teaspoon, but more than that and people will KNOW.

Since this is a gluten free + egg free recipe, the baking powder is there to provide lift (only a little because oatmeal cookies don’t really rise). If you’re all out of baking powder, you can make your own.

Alternatively, you can use 1/2 tsp baking soda + an acid (apple cider vinegar is the best choice), and still get a little lift.

Will this pumpkin cookie recipe turn out well even though there’s no xanthan gum?

Yes!! Great news, well, not great, but you get the idea. I personally have a severe, life threatening corn allergy. That means a LOT of ingredients are off the table, including most xanthan gum.

I’ve been able to own and operate an award winning GF + free-from bakery, all without xanthan gum. Now, I did tinker with guar gum at one point, but when I did side by side comparisons (even with a freeze and thaw test), the guar gum didn’t have a meaningful impact.

Here’s why: I don’t call for gluten free all purpose flour. Instead, I make a custom gluten free flour blend for all of my recipes. This means there’s balance from the start, and you don’t need dough conditioners and enhancers and additives to boost the results. In the case of this chewy cookie recipe, even though there’s limited gluten free flours, they’re in perfect balance with the sugar and supporting ingredients, so you don’t need extra bits and bobs to get them to work well.

As long as you follow the recipe as-is, yes, your chewy gluten-free pumpkin cookies will turn out beautifully, even without xanthan gum, guar gum, and all their friends.

Is a cookie sheet the same thing as a baking tray?

A cookie sheet and a baking tray (also called a baking sheet) are similar, but not quite the same. Unfortunately, a lot of homemade cookie recipes online use the terms interchangeably. A baking tray is solid, without holes, and generally has some weight to it, which prevents warping. It’s also usually dishwasher safe.

On the other hand, a cookie sheet is lighter, usually doesn’t have a lip/raised border, and often has small holes all over to promote better airflow. These slight changes allow for most cookie dough balls to bake up to cookie perfection.

In terms of if you’ll see a huge difference between the two, that’s going to depend on the cookie recipe. Some genuinely require improved airflow to perform their best. If you’re following my recipe, know that for the best cookies, you’ll only need a standard baking tray.

Do you have savory recipes that include pumpkin?

Why yes I do. You’ll find them all on RAISE, my membership site. Here’s the link for the savory recipes with pumpkin. Of course they’re all gluten-free pumpkin recipes, but they’re also dairy-free recipes, egg + nut + soy free recipes and so much more. If you’re more than gluten free, be sure to use the Advanced Recipe Search instead. Type pumpkin in the search box, then mix and match over 100 filters for your dietary needs, then hit the search button.