Chocolate Chip Protein Cookies | Almond Flour

Chocolate Chip Protein Cookies | Almond Flour

These chocolate chip protein cookies are made with almond and coconut flours, and pack 6 grams of protein per cookie.

Chocolate chip protein cookies in a small stack with one cookie facing forward, broken.

What do these chocolate protein cookies taste like?

These cookies are not exactly like decadent sugar-filled thick and chewy chocolate chip cookies. But they’re rich and buttery-tasting, with almost no added sugar, and packed with protein.

The texture is crisp and chewy at the same time. For a chewier cookie, try baking them for 8 minutes instead of 10 minutes. And keep them in a sealed plastic container at room temperature.

I’ve been curious about Lenny & Larry’s protein cookies (especially the chocolate chip variety), but their original formulation is made with wheat flour. They also have quite a bit of sugar, so I wouldn’t likely have been tempted to eat them anyway.

I’ve just noticed that Lenny & Larry’s now sells a “keto” variety made with almond flour, and erythritol (but in a facility shared with wheat). I guess I kind of unintentionally backed into a Lenny & Larry-style keto recipe? ?‍♀️

Overhead image of one chocolate chip protein cookie, with a corner broken.

Which protein powder is best?

Since I developed the bread recipes in my book Gluten Free on a Shoestring Bakes Bread, I’ve loved baking with whey protein isolate. It’s a nearly-pure form of protein powder that, when heated in the oven, behaves much like gluten.

Since I bake the bread recipes from that book quite often, I always have a lot of whey protein isolate in my pantry. I use it to bake my oat-based protein cookies, protein granola, and now these chocolate chip protein cookies.

Instead of protein powder, you can try using collagen powder for a huge nutritional boost with no added flavor at all. I really like Vital Proteins Collagen Peptides and Perfect Hydrolyzed Collagen Peptides (Those are affiliate links, but feel free to shop around for the best price.)

You can also try using your favorite flavored protein powder, like I like Vega essentials chocolate flavor protein powder like I use in our homemade protein bars. Those protein powders have other added ingredients, though, so it will have more of an effect on the outcome. That’s more of an experimentation!

Chocolate chip protein cookies raw on baking tray, about to go into the oven.

Which sugar alternative is best?

You don’t have to use a sugar alternative in these cookies, and can instead simply use 1/2 cup (100 g) granulated sugar. I prefer to use a sugar alternative rather than take a wholesome recipe and taint it with refined sugar.

I have been baking more and more with Lankato brand monk fruit granulated sugar alternative, and have had great results. I had been buying it on Amazon, but even found it at my local Costco recently for a better price.

You can also probably use a simple granulated erythritol sweetener, but the Lankato monk fruit blend (which contains monk fruit sweetener and erythritol) has a smoother taste. The monk fruit helps neutralize the cooling sensation that erythritol tends to cause.

Chocolate chip protein cookies baked on tray, just out of the oven.

Ingredients and substitutions

Dairy: There is dairy in these cookies in both the butter and the whey protein isolate. There are so many versions of protein powders available. Please see the full discussion above of my favorite ones.

It’s easy to replace the butter in these cookies with virgin coconut oil, melted and cooled. Just measure it out gram for gram. The butter gives these protein cookies a depth of flavor that the coconut oil is missing, but the almond flour nearly makes up for its absence.

Almonds: The base of this recipe is finely-ground blanched almond flour. If you can’t have almonds, you can certainly substitute cashew flour for the almond flour.

If you can’t have nuts at all, you can try using sunflower seed flour, but the cookies will almost certainly have a (harmless) greenish tint to them. If you can’t have almonds but can have peanuts, try my peanut butter protein cookies, which are made with peanut butter and whey protein isolate.

Eggs: There are two eggs in these cookies, so it’s worth trying to replace each of them with one “chia egg” (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel).

Coconut flour: There is no reliable alternative to coconut flour, but there are times when I’ve had success using twice as much tapioca flour (by weight) in place of coconut flour. I haven’t tried that in this recipe, though, so it’s a risk.

Xanthan gum: Adding a bit of xanthan gum to this recipe helps the cookies (and the dough) hold together well, and helps the cookies stay fresh for longer. It’s not essential.

Molasses: The single tablespoon of molasses in these cookies gives them that authentic chocolate chip cookie taste that normally comes from baking traditional chocolate chip cookies with brown sugar. You can replace it with a liquid alternative sweetener, like Lankato brand monkfruit maple syrup alternative.

Chocolate chips: I really like Lily’s Sweets brand stevia-sweetened chocolate baking chips. They seem to be much more widely available than they used to be, which I appreciate because mail-ordering chocolate can be risky in the warmer months. ☀️ 

Chocolate chip protein cookies stack of cookies with the top one broken.

These chocolate chip protein cookies are made with almond and coconut flours, and 6 grams of protein per cookie.

Like this recipe?

Prep time: Cook time: Yield: 15 cookies


1 1/2 cups (180 g) finely-ground blanched almond flour

1/4 cup + 1 tablespoon (30 g) coconut flour

1 scoop (30 g) whey protein isolate powder

1 teaspoon xanthan gum (optional)

1/2 teaspoon baking soda

1/4 teaspoon kosher salt

1/2 cup (100 g) Lankato monk fruit granulated sweetener

4 tablespoons (56 g) unsalted butter, melted and cooled

2 eggs (100 g, weighed out of shell) at room temperature, beaten

1 tablespoon (21 g) molasses

2 to 3 ounces sugar free chocolate chips, like Lily’s brand


  • Preheat your oven to 325°F. Line a large rimmed baking sheet with unbleached parchment paper and set it aside.

  • In a large bowl, place the almond flour, coconut flour, protein powder, optional xanthan gum, baking soda, salt, and granulated sweetener, and whisk to combine well. Create a well in the center of the dry ingredients, and add the butter, eggs, and molasses, and mix to combine well. Use the back of the mixing spoon to press the wet ingredients into the dry ones, turning the dough over until the dry ingredients have been completely absorbed. The dough will be thick and sticky. Add 2 ounces of the chocolate chips, and mix until evenly distributed throughout the cookie dough.

  • Using a spring-loaded ice cream scoop or two spoons, scoop the dough into portions about 1 1/2 tablespoons each. Using moist hands, roll each piece of dough into a round, press into a disk about 1/4-inch thick and place about 1 1/2-inches apart from one another on the prepared baking sheet. Top the rounds of cookie dough with some of the remaining chocolate chips, as desired.

  • Place the baking sheet in the center of the preheated oven and bake until the cookies are set in the center and are just beginning to brown around the edges, about 10 minutes. Remove the cookies from the oven and allow to cool on the baking sheet until firm, about 10 minutes. Store in a sealed plastic container at room temperature for at least 3 days or freeze for longer storage.

  • Approximate nutrition information per cookie:

    150 calories | 11.9 g fat | 16.8 g Total carbs | Dietary Fiber 6.2 g | Protein 6.1 g

    Nutrition and Calories for chocolate chip protein cookies



Where should I send your free guide?

By entering your email, you're agreeing to our Privacy Policy. We respect your email privacy, and will never share your information.