Gluten Free Chocolate Cookie Recipe (Vegan Cookies)

Last Updated on September 22, 2026 by The Allergy Chef

It’s another great day to bake gluten free cooookkkiiieeessssssss!! Alright baking buddy, today it’s all about gluten free chocolate cookies that are loaded with chocolate flavor and a cool minty finish. This easy recipe is perfect for the holiday season since it comes together pretty quickly, and the little candies are so dang cute.

If you manage Celiac Disease, a wheat allergy, or NCGS, not only will you love these gluten free chocolate cookies, but you can share them with your dairy free friends, vegan friends, nut free friends, and more. These bad boys are top 9 free, top 14 free, and more, making them seriously inclusive. Heck yes!

One of my tasters said that this is the kind of cookie you want to enjoy with a glass of milk, and if I weren’t allergic to all of this, I’d probably agree. And on that note, let’s get to baking.

Table of Contents

Gluten Free Cookie Fanatics Celebrate! I’ve got so many amazing gluten free and allergy friendly cookie recipes for you to dive into. If you need more, you can pick up a copy of my Gluten Free + Allergy Friendly Cookes & Desserts Cookbook.

Allergy Status (Includes Top 9 Free Mint Candies)

Free From: Wheat/Gluten, Dairy, Egg, Soy, Tree Nuts, Peanut, Fish, Shellfish, Sesame, Top 9 Allergens, Top 14 Allergens, Alliums, Apple, Avocado, Banana, Beans & Lentils, Berries, Buckwheat, Carrot, Celery, Cinnamon, Citrus, Coconut, Cruciferous, Garlic, Latex Cross Reactive Foods (H/M), Lupin, Mushroom, Mustard, Nightshade, Oat, Onion, Pea & Pea Protein, Potato (Nightshade Variety), Poultry, Red Meat, Squash & Gourd, Stone Fruits, Strawberry, Sweet Potato & Yam, Tapioca/Cassava/Yuca/Manioc, Tomato, Yeast

Friendly To: EOE, Vegan

No Whey Chocolate Peppermint No-Nos Ingredients: Vegan Cane Sugar, Cocoa Butter, Rice Syrup Powder, Unsweetened Chocolate, Sunflower Lecithin (Emulsifier), Gum Arabic, Carnauba Wax, Pectin, Spirulina Extract (Color), Fruit and Vegetable Juice (Color), Natural Peppermint Oil

Tools Needed for This Gluten Free Chocolate Cookie Recipe

Kitchen Scale (this is the one that I love)
Small Bowl (for flax gel OR whisked egg)
Stand Mixer with Paddle Attachment OR Electric Hand Mixer + Large Bowl
Baking Tray
Parchment Paper
Spatula (this is the one that I really like)
Cookie Scoop

Ingredients for This Gluten Free Chocolate Cookie Recipe

Flax Gel/Bind

4 TBSP Golden Flax Meal (use this brand for best results)
8 TBSP Water (room temperature)

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

Part 1 Ingredients (Wet Ingredients)

225g Unsalted Butter OR Dairy Free Butter, also called vegan butter (8 ounces) room temperature, but not super soft
300g Organic Dark Brown Sugar
75g Organic Cacao Powder

Part 2 Ingredients (Dry Ingredients)

OK, dry ingredients and vanilla extract, but you get the idea.

230g Sorghum Flour, superfine
50g Millet Flour, superfine
40g Arrowroot
3 tsp Baking Powder
2 tsp Organic Vanilla Extract
1 tsp Sea Salt

Part 3 Ingredient

4 packs No Whey Chocolate Peppermint No-Nos Candies (this is a dairy free, vegan, top 9 free faux m&m product)

Ingredient Notes & Substitutes

Flax: If you’re not vegan and you’re not allergic to eggs, you can substitute this with 1 large egg or 2 small/medium eggs that are well whisked. When I call for the flax gel, pour in your whisked egg instead.

Dark Brown Sugar: This is a granulated sweetener with a bit of molasses in the mix. The only sugar substitutes that will work are other granulated sweeteners (light brown sugar, white sugar, caster sugar, maple sugar, coconut sugar, date sugar, and so on). Liquid sweeteners (maple syrup, agave, etc.) will not work and will ruin your gluten-free chocolate cookies.

Keep in mind, if you make this swap, you’ll be losing some of the depth of flavour, or if you choose an unrefined sweetener, you’ll lose some of the natural sweetness in these cookies. It won’t be the end of the world, but I also want to make sure you’re aware.

Cacao Powder: This is not the same thing as cocoa powder or Dutch-processed cocoa powder. It’s an organic, minimally processed form of chocolate powder with an intense rich flavour. For best results, don’t swap this for something else.

Gluten Free Flour Blend: This gluten free cookie recipe uses 320g of a gluten-free flour blend. You can swap my blend for an all purpose flour if needed. Just know that you’ll shift the flavor and possibly the texture a small amount when doing so. Also, you’ll need to test if your cookies can still freeze and thaw well, as not all GF flours hold up to the freeze thaw test.

You can combine flour at home to make a custom GF AP blend, or use a commercial blend. Do not swap the flours for a single flour including almond flour, cassava flour, coconut flour, tiger nut flour (tiber, not a tree nut), bean flours, nut or seed flours, and so on. It needs to be a proper all purpose flour that you know will be successful in a cookie situation.

Gluten Free Chocolate Cookie Directions

Oven Temperature: 325f/163c
Bake Time: 14 – 16 Minutes
Cool on Tray Time: 15 Minutes

Before we jump into the recipe instructions, preheat your oven 🙂 Also, watch the video if you’d like to see how this gluten free chocolate cookie comes together.

First, stir your flax and water together in a small bowl and set aside. If you’ll be using eggs, whisk them well in a small bowl and set aside. This is also a good time to preheat your oven if you haven’t already.

For cookies, I use a stand mixer with the paddle attachment. If you don’t have a stand mixer, use a large mixing bowl (a medium bowl will be too small) with an electric hand mixer or whisk + wooden spoon or spatula. Just know, that whisk method will require some elbow grease.

Place your empty mixing bowl on your kitchen scale, tare to zero, and add your Part 1 Ingredients.

Cream butter, cacao, and sugar together (mix) on medium speed for 30 seconds. Turn the mixer off, scrape down the bowl, and return it to your scale. Tare and add the Part 2 Ingredients. Don’t forget to tare between weighted ingredients.

Pulse on low speed to combine, and when enough of the flour is wet, turn the mixer on medium speed (this prevents a huge mess). Mix until a nice cookie dough forms. Turn the mixer off, add the flax gel, and mix one last time.

Turn your mixer off and fold in most of your candy. Reserve some candies for placing on top before baking. If you use your mixer to add the candy, the pieces will break and be little chunks like chocolate chips in the dough. You can do that, but if you want whole pieces, they need to be folded in with a spatula or wooden spoon.

Line a baking tray with parchment paper, and use a medium or large cookie dough scooper to portion out your dough. Roll your portions into balls, then press down your cookie balls about half way. Place a few candies on top to decorate.

Bake at 325f/163c for 15 minutes. Allow the cookies to cool on the tray for 15 minutes before transferring or enjoying.

How to Tweak These Chocolate Cookies

At its core, this is an amazing gluten free chocolate cookie recipe. You can skip the mint candy and have JUST a delicious chocolate cookie. You can add chocolate chips and have chocolate chocolate chip cookies, and the list goes on. Now, here are some very fun ways you can tweak this gluten free vegan cookie recipe:

Drizzle melted chocolate or melted white chocolate on top of your cookies for an awesome pop of flavour.
Skip the mint candy and add some organic espresso powder for a coffee chocolate cookie. You’ll also need to add a little milk of choice to keep the moisture content just right.
Skip the mint candy and make spicy chocolate cookies instead. Add up to 1 teaspoon of organic cayenne pepper to the cookie dough batter. You can also make a spicy chocolate glaze with organic powdered sugar, cayenne pepper, organic vanilla extract, and water.
Omit the candy and drizzle a smoky caramel sauce on top and garnish with a pinch of flaky sea salt for a chocolate salty caramel experience.
Exchange the mint candy for these gluten free, allergy friendly vegan salted caramel chocolate chips instead for a fantastic flavor combination.
Leave out the mint candy. Make a glaze with freeze dried fruit powder for a fruity chocolate cookie experience. Strawberry and banana would be real crowd pleasers.

Storage Notes for Your Gluten Free Chocolate Cookies

Once you have cooled baked cookies, it’s time to store them (assuming you didn’t eat them all with your kids, and no judgement if you did). 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). For best results, don’t store cookies in the refrigerator.

One of the best things about this recipe is that your cookies are freezer friendly. To freeze your gluten free chocolate cookies, place them in a single layer on your large baking tray lined with parchment paper. 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 oatmeal 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 flavor 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 minty treat and you can feel like it’s Christmas in July if you keep yourself well stocked.

More Delicious Gluten Free Recipes

If you’re on the hunt for more gluten-free cookies, or other awesome desserts, man oh man have I got you covered.

Vegan Snickerdoodle Cookies Recipe (these bakery-style cookies were a top seller at my gluten free, vegan, top 9 free bakery back in the day)
Soft Baked Gluten Free Gingerbread Cookie Recipe (another amazing gluten-free cookie recipe from my award winning bakery)
Gluten Free, Dairy Free Chocolate Pudding Recipe (awesome if you love chocolate recipes with a touch of healthy ingredients)
Fudgy Chocolate Brownie Recipe (gluten free, egg free, vegan, and more)

Answering Your Questions About This Gluten Free Chocolate Cookie Recipe

Can I use natural cocoa powder instead of the cacao powder?

You can try, but it certainly won’t be the same. In terms of how much to use, you’ll use the same 75g that I use for the cacao powder. This isn’t something I’ve personally tested, nor would I since I don’t use natural cocoa powder or anything of that nature.

I’d suggest making a half batch of these cookies, in case this swap doesn’t work out. I’d hate to see you lose loads of expensive ingredients.

Does this recipe make chewy cookies?

No, these cookies are not chewy at all. They’re almost like a soft baked cookie, but dense. I’m not sure how else to explain it, but they’re not super crunchy or anything of that nature.

Can I bake this as a cake layer?

Yup! Now, I don’t know what your baking time will be, but here’s what you’ll want to do. Use the same size cake pan as the actual cake, this way, you have a perfectly sized cookie layer.

Cut a parchment papery circle for the bottom of the pan so you don’t need to worry about sticking. You’ll also want to have a ring of parchment paper on the side of the cake pan. I’ve done this before with a lot of my gluten free cookie recipes and I usually have to use a Vitamix spatula to get the sides to release.

With your parchment paper in place, add a bunch of cookie dough and press it until it forms a nice even single layer, as tall or as short as you’d like it to be. Your baking temperature will still be the same, and I’d bake this for at least 22 minutes to start, then check on it, and add more time as needed.

The cool thing is that since you’ll have a longer bake time, you’ll also have really nice crisp edges on the larger cookie. Have so much fun with this!

Could I add crushed nuts to the cookie batter?

You can, but you’ll probably need to add a little milk of choice to make sure the moisture content is just right. The cookie dough batter is on the dense side, and chopped nuts are going to get you close to crumbling because the dough may not be able to really connect to itself well.

I’m not sure if I’m communicating this effectively, but basically, yes, you can, but if your cookie dough is hard to form, add a little milk of choice to loosen up the dough some. Maybe that was better…

In terms of which nuts, my top three picks for this recipe are pecans, cashews, almonds, assuming you’re leaving out the mint candies (or using chocolate chips instead of the candy). If you want to keep the candy and have crushed nuts, I’d only use cashews or almonds since pecans + mint aren’t all that awesome together.

Is this a good cookie recipe to share at a holiday party?

Oh. My. Goodness. YES. This is the perfect recipe to share at a holiday party because you have the dairy-free option, making this gluten free chocolate cookie super inclusive. It’s vegan, top 9 free, and more. You could literally show all your friends what the gluten free good stuff is all about.

I’ll also assure you: people without food allergies are part of my taste testing group. I never post a recipe that isn’t well received, so, the friends at your holiday party will be very happy you decided to share these gluten free cookies with them.

Could I swap the mint candies for chocolate chips?

Yes you absolutely can use chocolate chips in this chocolate cookie recipe. You can use milk chocolate chips, dark chocolate chips, white chocolate chips, vegan salted caramel chocolate chips, or anything else in between. white chocolate chip cookie

At that point, you’d have gluten-free chocolate chip cookies and they’d taste fabulous, especially when warm and the chocolate chips are a little bit melty. Also, as you dig into your double chocolate cookies (especially if you have a little one) make sure you guys take a moment to be a proper Cookie Monster together. Like, don’t make a HUGE mess, but have a little fun.

Oh! You know what else you could do… Use mini chocolate chips in the batter and then use a small cookie scoop instead of medium or large. Make the cutest little cookies and use them as a little afternoon treat in a lunch box, or for super cute mini ice cream sandwiches.

Can I make this gluten free cookie recipe in my food processor?

Not really. I mean, technically, you can make this chocolate cookie recipe in your food processor, but you won’t get the perfect texture in the end. Not only that, but you’d have to make 25 – 50% of the recipe since it won’t all fit into your food processor.

The reason this isn’t the best choice is the blade. A food processor is excellent for things like pie crust and power balls (aka protein balls). If you were to use it for this cookie dough recipe, it would kind of create something similar to power balls, rather than cookie dough.

Now, if you want to make something like granola butter, you absolutely could use this chocolate cookie recipe as a base and use the food processor, then fold in the optional mix-ins at the end. For a more traditional granola butter, you’d want to add gluten free rolled oats to your blend

However, I’m going to assume you want cookies, and tell you that if you don’t have a stand mixer, the next best thing is a large mixing bowl + an electric hand mixer. If you don’t have one, you can mix by hand with a whisk, but it’s going to take some elbow grease.

Which vegan butter is the best for this cookie recipe?

Fun fact! Whilst there are a lot of dairy-free milk and dairy-free butter options on the market these days, I haven’t tried most, and for good reason. My goal is to always include the most amount of people possible, so I always use the Earth Balance food service box that’s top 9 free and coconut free.

Commercially, you can choose from Country Crock, Earth Balance (their line is HUGE), Melt, and a few others. You can read about the different dairy free and vegan butter options in my Ultimate Guide to Dairy Free Substitutes. I’ve linked you to the butter section, and there are notes on other major allergens.

If I were in a situation where I didn’t have taste testers allergic to coconut (most contain coconut these days), I’d do a side-by-side comparison just to know what people think.

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, go on vacations 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 gluten free cookie in the end.

Will this make an edible gluten free chocolate 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 this egg free and gluten-free cookie dough, 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 cacao is optional, and totally not necessary.
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 gluten free chocolate cookie recipe as instructed. When it’s time to add the flour, add your cooled roasted flour.
When the cookie dough is ready, now you have a proper, safe, edible cookie dough.

Whilst you can store your edible dough on the counter, I suggest storing your edible dough in the fridge. It’s OK to leave some 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 tasty treat.

It’s up to you if you still include the mint candy, or just leave this as a straight chocolate cookie dough. You can also swap for chocolate chips and have a chocolate chocolate chip cookie situation on your hands (in a very good way).

Do I need to chill these chocolate cookies before baking?

Great news! There’s no chilling time required, so you can skip the fridge and get straight to 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 cookies on a cooling rack. Just allow them to cool on the baking tray for 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 (sorghum + millet + arrowroot in this case) for something like Bob’s Red Mill All Purpose Gluten-Free Flour (or King Arthur’s 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.

Also, remember, this is a chocolate cookie recipe, so don’t change the cacao for anything.

Will this gluten free oatmeal 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 these gluten & dairy free chocolate cookies, 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 oatmeal cookies will turn out beautifully, even without xanthan gum, guar gum, and all their friends.

Can I use baking soda instead of baking powder?

Nope, and I’m so glad you asked because they aren’t the same type of leavening agent. 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 (it’s not a tonne). If you’re all out of baking powder, you can make your own.

Alternatively, you can use 1/2 tsp baking soda + an acid in this recipe (apple cider vinegar the best option), and still get a little lift. It won’t be the same, but you’re still going to enjoy these gluten-free chocolate cookies.

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.