In elementary school, my friends and I always looked forward to lunch. When that initial bell rang, we dashed out to the brown picnic tables, unzipped our brightly colored lunch totes, and start nibbling on the fruit and sandwiches our parents had packed in foil and zip-topped baggies.
As a picky eater, I knew I could count on Mom and Dad to only include my favorite entrées and sides: half of a plain whole wheat peanut butter sandwich, half of a bagel with cream cheese, apple slices, orange slices, or grapes. I was boring and predictable when it came to savory options!
But when it came to my sweet treat, I let them surprise me. I wouldn’t turn up my nose at any type of sugar! They tucked in an assortment of Little Debbie desserts, Chewy Chips Ahoy, Oreos, Keebler elves, and occasionally homemade cookies. (The love-of-baking gene mostly skipped my mom!)
Most of my friends’ parents packed similar sweets, so we usually traded treats at the end of the meal depending on what we felt like that day. We sometimes negotiated for full desserts (one Little Debbie oatmeal crème pie for two Keebler elves!), but more often, we split our sweets instead.
Whoever brought homemade cookies automatically became the most popular kid at the table. Soft, thick, chewy, and full of partially melted chocolate chips from sitting out in the sun at the picnic tables… Those were rarely split or shared, especially when they appeared in my lunch box—it was such a rare occasion!
My mom usually followed the recipe on the back of the Toll House bag of chocolate chips, but since I grew up to be a healthy baking blogger, that didn’t quite work for me anymore! I created my own lightened-up version over a year ago (it’s one of the most popular recipes on the blog!), and today I decided to tackle a bigger challenge: The Ultimate Healthy Gluten-Free Chocolate Chip Cookies!
Yes, the ultimate. Not just good, not just great… The cream of the crop, the best of the best, the recipe that tempts you to sneak one from the cookie jar every time you glance at the kitchen. The cookies that melt in your mouth and taste like little bites of pure bliss.
I have really high standards when it comes to chocolate chip cookies. Perhaps you can tell?… 😉
HOW TO MAKE THE BEST HEALTHY GLUTEN FREE CHOCOLATE CHIP COOKIES
So let’s talk about how to make the best healthy gluten-free chocolate chip cookies! I learned a LOT about how to make the perfect gluten-free cookies in my many rounds of recipe testing, so let’s cover those important details.
The most important part of this recipe is the gluten-free flour blend. Many gluten-free flours can be coarse or grainy, and they often pass off that texture to the finished baked goods. But I didn’t want grainy cookies—I wanted ones with the same soft and chewy texture as regular cookies!
So I tested and tweaked my gluten-free blend umpteen times. I started with millet, brown rice, and tapioca flours, but both of the former ones have that pesky coarser texture. It isn’t noticeable in muffins and cakes, but it’s extremely prominent in cookies! After a few rounds of substituting certain flours and decreasing others, I finally came up with my perfect trio: millet, tapioca, and coconut flours.
Coconut flour ended up being the missing piece of the gluten-free flour puzzle! It isn’t grainy, like many others, and it gave the cookies the smooth texture they needed. However, it is 3 times as absorbent as regular flour, so it is extremely important that you measure it correctly. (I highly recommend a kitchen scale for this!) Any extra coconut flour will dry out your cookies and make them cakey.
Gluten provides structure to baked goods and keeps cookies chewy, so flours without it require an extra ingredient that imitates these properties: xanthan gum. You can find xanthan gum on the baking aisle near the gluten-free flours. It costs a little more than other ingredients, but that small bag will last a long time. (I bought mine a year and a half ago, and I’ve barely used ¼ of the bag!)
Unlike traditional recipes, you must chill this cookie dough and let it rest. Like we talked about before, coconut flour is more absorbent than regular flour, so we need to give it time to absorb the moisture. Chilling also makes the cookie dough stiffer so it won’t spread as much while baking.
For the thickest cookies, drop the cookie dough into rounded scoops that are about as tall as they are wide. (It’s much too sticky to roll into balls between your palms, so please don’t bother to try!) The cookie dough spreads some while baking, but the taller the mounds are, the less they’ll flatten. For thinner, wider cookies, gently flatten the scoops of cookie dough with a spatula before baking.
Just look at those gorgeous beauties! Soft, chewy, and chock full of melty chips… That’s definitely my idea of bliss! And for quality control, I had to eat 3 fresh from the oven. You know, just to be extra sure.
And these cookies definitely passed with flying colors! When you make your own, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! 🙂 ) I’d love to see your healthy gluten-free chocolate chip cookies!
The Ultimate Healthy Gluten-Free Chocolate Chip Cookies
Ingredients
- ½ cup (60g) millet flour (measured like this)
- ½ cup (60g) tapioca flour (measured like this)
- 6 tbsp (42g) coconut flour (measured like this)
- 1 ½ tsp xanthan gum
- 1 ½ tsp baking powder
- ¼ tsp salt
- 4 tbsp (56g) unsalted butter, melted and cooled slightly
- 2 large eggs, room temperature
- 4 tsp vanilla extract
- 1 cup (192g) coconut sugar or light brown sugar (see Notes!)
- 4 tbsp (56g) semi-sweet chocolate chips
- 2 tbsp (28g) miniature chocolate chips, divided
Instructions
- In a medium bowl, whisk together the millet flour, tapioca flour, coconut flour, xanthan gum, baking powder, and salt. In a separate bowl, whisk together the butter and eggs. Whisk in the vanilla. Stir in the sugar, smearing out any clumps along the side of the bowl. Add in the flour mixture, stirring until incorporated. Fold in the semi-sweet chocolate chips and 1 tablespoon of miniature chocolate chips. Chill the cookie dough for 30 minutes.
- Preheat the oven to 350°F, and line two baking sheets with silicone baking mats or parchment paper.
- Drop the cookie dough into 24 rounded scoops onto the prepared baking sheets. Gently press the remaining miniature chocolate chips into the tops. Bake at 350°F for 10-13 minutes. Cool on the baking sheets for 10 minutes before turning out onto a wire rack.
Notes
View Nutrition Information + Weight Watchers Points
Hi Amy!
Quick question on types of flours and starches. In this recipe could I substitute the millet flour with brown rice flour?
Also wondering about the whole eggs…instead of 2 whole eggs, would 4 egg whites work?
Thanks so much!
Vanessa
I really appreciate your interest in my recipe Vanessa! That flour substitute will make the cookies taste a little grainy. Trust me — I tried that! 😉 I’d also recommend using 2 full eggs to ensure the cookies turn out with the correct texture. I’d love to hear what you think if you try these!
Will do! Thanks Amy. 🙂
My pleasure Vanessa! 🙂
Hey…both my kids loved these cookies and said it was a keeper. They have. It been fans of some of the clean eating desserts so this is great!
I did have to substitute the millet flour and used oat flour in its place. I did not have any xtar gum so I just omitted that.
The dough stayed in the refrigerator probably close to 2 hours. We flattens on the cookie sheet and they were great.
Oh yeah one more indirect thing from the ingredients I did not measure the chips! Lol
I just poured it in to my liking so there was plenty!
Thank you.
YAY!! I’m really glad your kids loved these — and I’m truly touched that they called this recipe a keeper! What a huge compliment Robin! 🙂 The xanthan gum will make the cookies a little chewier. I’ve also heard that sorghum flour is also a great substitute for millet flour (just if you’re looking to avoid the “oatmeal cookie” flavor!). And as a huge chocoholic, I’m always a fan of extra chocolate chips! 😉
Could we substitute the egg with chia or flaxseed? My daughter cannot eat egg protein so we could even do 2 egg yolks with the flaxseed?
I really appreciate your interest in my recipe Sunya! My brother is actually allergic to eggs and can’t eat them either, and Ener-G is my favorite substitute. Ener-G is a shelf-stable powder that keeps for ages. It works perfectly as an egg replacer in nearly all of my recipes, including this one! For my recipes, use 1 ½ teaspoons Ener-G + 2 tablespoons warm water for each egg white, and you’ll need an additional ½ tablespoon of butter or coconut oil {or Earth Balance, if you’re vegan!} for each egg yolk.
Alternatively, I actually have a completely egg-free version of these cookies here! Maybe that would be even better suited to your daughter’s dietary needs? 🙂
I can’t wait to hear what you think of either version of these cookies if you end up making them!
Thank you so much Amy, I will try them!! It’s tough but not impossible to go egg free and gluten, rice and oat free so I love your gluten free flour recipe that has no rice/oats in it.
It’s my pleasure Sunya! I’m always happy to help! 🙂 I’m really excited to hear what you think of the cookies!!
I made these. The texture was amazing. Very surprised at how well they turned out and so grateful as I can’t rice or gluten. Would this work in a loaf/muffin?
I’m so glad you loved these cookies Olivia! That really means a lot to me. Thank you for taking the time to let me know too! 🙂 Unfortunately, this recipe won’t work as a loaf or muffins. However, I have LOTS of muffin recipes that can easily be made gluten-free (and rice-free as well!). You can find all of them here, including my chocolate chip mini muffins recipe here. If you can have sorghum flour, that would probably be the best substitute for the brown rice flour in the gluten-free blend I typically recommend in my muffin recipes. I’d love to hear what you think if you try making those chocolate chip mini muffins — or any of my other muffin recipes!
Thanks! I’ll try the sorghum substitute!
It’s my pleasure Olivia! I can’t wait to hear what you think! 🙂
I got around to making an egg-free banana bread with the sorghum substitute. Worked great! Thank you so much. It’s now copied down in my recipe book and it will be a keeper for all my gluten free muffin projects 🙂
I’m so excited to hear that, Olivia! Thank you so much for taking the time to let me know — that really means a lot. 🙂 I’m so honored that you’d call it a keeper! That’s the best kind of compliment!
Can I replace the butter with applesauce? Also, what other flour can I replace coconut flour with as I’m on a fat free diet
I really appreciate your interest in my recipe Raghda! I typically don’t recommend substituting applesauce for the butter because it’ll make these cookies very cakey and bready, rather than soft and chewy. However, if you aren’t allowed to have any amount of fat whatsoever, then you may — just keep in mind the texture will be different! Coconut flour produces the best texture, but if you aren’t allowed to have that either, then you can double the amount of millet flour and tapioca flour (so you’ll use 1 cup of each), but the texture will be a bit grainy. I’d love to hear what you think of these cookies if you try making them!
Hello Amy, I’m a Gluten Free baker as well. I recently have had health issues exclusive to my gall bladder so the less fat the better. In your Chocolate chip cookie recipe is there another flour or gf blend.I could use to avoid the coconut and nut flours? Thanks, tricia
I really appreciate your interest in my recipe Tricia! When I’ve used other GF flours instead of coconut flour, these cookies had a slightly grainy texture. Given your situation and how you aren’t able to have nuts, we could try to substitute another flour, but just keep in mind that these cookies will end up with that somewhat grainy texture as a result.
What flours do you currently have and use?
I’m so sorry I’m just now responding too. I had some family things I needed to take care of, but I’m still happy to help figure out how to modify this recipe to suit your needs! 🙂