Grain-Free Chocolate Chip Cookies (Soft, Chewy & Gluten Free)

There is absolutely nothing cozier than a warm chocolate chip cookie, and these grain-free chocolate chip cookies hit that sweet spot between nostalgic bakery cookie and better-for-you ingredients.

If you’re new around here, I’m always trying to land in that space where comfort food meets clean ingredients. These cookies are exactly that. They’re soft in the center, lightly crisp on the edges, speckled with melty chocolate, and yes… finished with flaky salt because we’re fancy like that.

The best part?
No one ever guesses they’re made without regular flour.

They bake up beautifully golden, and unlike many almond flour cookies that crumble or feel sandy, chilling the dough and whisking the sugar into warm butter creates a smooth, cohesive, bakery-style texture. You’ll taste hints of caramel from the coconut sugar, a subtle nutty warmth, and that perfect salty-sweet bite.

Serve them as after-school snacks, in cookie jars, for Christmas gifting, as meal prep desserts, or eat one straight off the tray. I won’t tell.

If you’re more of a classic-cookie person too, don’t worry; I have a traditional soft & chewy chocolate chip cookie recipe you’ll love right here.

Why You’ll Love These Cookies

Soft-baked + chewy (not cakey or crumbly)
Naturally grain-free, gluten-free, and refined ingredient friendly
1 bowl for dry, 1 bowl for wet — minimal cleanup
Dough chills fast for thick cookies with clean edges
Kid-approved, adult-obsessed
Freezer friendly for quick treats

If you love almond flour baking but want a cookie that actually holds its shape and has that classic chocolate chip bite, this recipe is your new go-to.

Ingredients

Almond flour – the soft, buttery base that keeps these cookies grain-free and tender without tasting “healthy.”

Coconut flour – a tiny addition that strengthens the dough, prevents crumbling, and gives structure to the cookie.

Baking soda – offers gentle lift and helps create that soft-baked, chewy bite.

Fine sea salt – balances the sweetness and enhances the warm, caramel-like flavors.

Coconut sugar – adds that cozy brown-sugar flavor and gives the cookie its golden hue.

Melted butter – provides richness, chew, and that classic cookie texture (even without gluten).

Egg – binds the dough and ensures the cookie stays soft rather than sandy.

Vanilla bean paste – elevates the flavor with real vanilla flecks; it makes the cookies taste bakery-style.

Dark chocolate chunks – melt into pockets of chocolate that make every bite indulgent.

Flaky sea salt – an optional finishing touch that makes the sweetness pop and adds a gourmet touch.

Ingredient Swaps

Dairy-free? -> Swap the butter for melted coconut oil; the cookies will be slightly softer but still delicious.
No coconut flour? -> Simply add a few extra tablespoons of almond flour to maintain structure.
Out of coconut sugar? -> Brown sugar or maple sugar works seamlessly and gives nearly identical flavor.
No vanilla bean paste? -> Use vanilla extract; you’ll lose the speckles, but the flavor remains warm and sweet.
Want lower sugar or lower glycemic options? -> Use allulose or monkfruit; the cookies may spread a little more, but they stay soft and chewy.

How to Make Grain-Free Chocolate Chip Cookies

Step 1: Melt the butter

Warm, not hot, butter gives you richer flavor and helps dissolve the sugar without cooking the egg later.

Step 2: Whisk sugar into melted butter

This step dissolves the coconut sugar slightly, creating a glossy base that helps the cookies hold together and bake evenly.

Step 3: Add egg + vanilla

Room-temperature egg blends easier and prevents the butter from seizing.

Step 4: Combine dry ingredients

Mixing them separately ensures even distribution so your cookies bake consistently.

Step 5: Make the dough

Fold until thick, then add chocolate chunks; this keeps the dough tender and prevents overmixing.

Step 6: Chill

This improves cookie thickness, prevents overspreading, and gives you that chewy center.

Step 7: Bake

Watch for edges turning golden and centers looking slightly soft — that’s the sweet spot for tenderness.

Step 8: Finish + cool

A sprinkle of flaky sea salt adds contrast, and cooling allows the cookies to set without drying out.

Tips for the Best Grain-Free Cookies

Flatten before baking — almond flour cookies don’t spread as much as wheat-based doughs.

Don’t skip the chill — it changes everything about the texture.

Cool on the tray first — this helps the bottoms firm without becoming dry.

Use high-quality chocolate — it makes a noticeable difference since each bite depends on it.

Storage & Freezing

These cookies store beautifully, making them ideal for meal prep or gifting:

Room temp: up to 3 days in an airtight container
Refrigerator: up to 1 week — they stay chewy!
Freezer: 2–3 months baked or unbaked

To bake from frozen, add an extra minute to your bake time.

Frequently Asked Questions

Why do my almond flour cookies fall apart?

They typically need more chill time; or an extra tablespoon of almond flour if your brand is extra fine.

Why didn’t my cookies spread?

Either your butter cooled too much or your dough wasn’t chilled long enough; shape with your fingers before baking.

Can I add protein powder?

Yes! Collagen or a small scoop of whey works, just add a tiny splash of butter if the dough feels dry.

Can I make these nut-free?

These are designed around almond flour, but sunflower seed flour or tigernut flour may work with adjustments.