Salted Chocolate Peanut Butter Thumbprint Cookies

Irresistible chocolate peanut butter thumbprint cookies! With a soft peanut butter base, a chocolate peanut butter filling and a touch of flaky sea salt! Vegan & gluten free!

A small plate with three Chocolate Peanut Butter Thumbprint Cookies with more cookies and coffee in the background.

It’s time to get our bake on! We’ve had a week or so to settle and eat plenty of veggies after all that thanksgiving feasting. And now, now, we are ready to dive on in to holiday baking central (!!). 

First up? These salted chocolate peanut butter thumbprint cookies.

Yup, that name is totally a mouthful.

But! I was so hesitant to leave any of it out because ALL components are essential to the deliciousness that is these cookies. Let’s discuss.

  • We have a super simple & super tender peanut butter-y cookie base.
  • We have a two-ingredient dark chocolate / peanut butter filling.
  • We have a sprinkle of sparkle with flaky sea salt over the top.

All combining into two-bite nuggets of goodness that I made far more times than necessary in the name of “recipe testing.”

Umm, in the name of delighting my taste buds is more like it.

And when I finally stopped making them, even the husband was majorly disappointed. Cookie withdrawal to the max.

So, until we meet again my little cookies (hey there christmas!) … go forth and spread some holiday baking cheer!

{Oh, oh! I forgot to mention that these bad boys also happen to be gluten free and vegan. Which was completely accidental but kinda completely awesome because now EVERYONE can enjoy! I’m so lovin’ it.}

Chocolate Peanut Butter Thumbprint Cookies on a baking sheet with a bowl of melted chocolate.

Tips & Tricks For These Chocolate Peanut Butter Thumbprint Cookies

  1. I would encourage you to stick with natural (i.e. drippy) peanut butter for this recipe. I did not test the cookies with regular peanut butter, so I can’t say how it would work if you made the substitution.
  2. Along those lines, I would also encourage you not to go rogue and try to use different kinds of flour. PLEASE stick with the blanched almond flour / oat flour combo!! I use Bob’s Red Mill super-fine blanched almond flour and their oat flour (<— not sponsored! just what I use and would recommend). I tried these once with white whole wheat flour and almond flour and they just don’t turn out as well (the wheat flour overpowers all the other flavors).
  3. A note on allergies – if you have any, please be sure to read ingredient labels! This is important with the dark chocolate chips, oat flour, etc.
  4. Even after chilling in the fridge, the dough will be on the softer side when rolling into balls. But it’s okay – just roll with it! (Ha! You know, as you literally roll it into balls.)
  5. And finally, let’s talk about the chocolate filling once you spoon it into the cookies. After setting for a short while, it will be more on the fudgy side. But after setting for a decent amount of time, it will harden up (i.e. so that you can stack them in a container for storage). But have no fear! The peanut butter keeps the chocolate “softer” when you bite into it – so it most definitely will not be super hard like a chocolate bar.

Chocolate + peanut butter all rolled up into one little bite? Oh heck yes. Christmas baking, I love you so.

Psssst. While I so think you should make these thumbprint cookies for the holidays, there are PLENTY more ideas in the cookie archives! I mean, can we ever have enough cookies? I think not friends, I think not.

Three Chocolate Peanut Butter Thumbprint Cookies on a plate with a bite taken out of one.

Additional Vegan Dessert Recipes You Might Enjoy!

Did you make this recipe? Rate and review it down below! I’d love to hear from you.

Salted Chocolate Peanut Butter Thumbprint Cookies

Salted Chocolate Peanut Butter Thumbprint Cookies

Yield: about 18 cookies
Prep Time: 1 hour 5 minutes
Cook Time: 12 minutes
Total Time: 1 hour 17 minutes

Irresistible chocolate peanut butter thumbprint cookies! With a soft peanut butter base, a chocolate peanut butter filling and a touch of flaky sea salt!


For the cookies:

  • ¾ cup plus 1 tablespoon blanched almond flour
  • ¾ cup plus 1 tablespoon oat flour
  • ⅛ teaspoon fine sea salt
  • ¼ cup melted coconut oil
  • ¼ cup pure maple syrup
  • 3 tablespoons creamy natural peanut butter (stirred well!)
  • 1 teaspoon vanilla extract

For the filling:

  • ½ cup dark chocolate chips
  • 2 tablespoons creamy natural peanut butter (stirred well!)
  • flaky sea salt, for sprinkling


For the cookies:

  1. In a medium bowl, whisk together the almond flour, oat flour and sea salt. In another medium bowl, whisk together the coconut oil, maple syrup, peanut butter and vanilla extract until smooth. Add the dry ingredients to the bowl with the wet and mix until combined. Transfer the bowl to the refrigerator and chill for 45 minutes.
  2. Meanwhile, preheat the oven to 350ºF. Line a large baking sheet with parchment paper and set aside.
  3. Shape the chilled dough into about 1 to 1 ¼-inch balls (about a heaping tablespoon of dough). Place on the prepared baking sheet about 1 ½ to 2 inches apart. Use your thumb (or a wine cork works really well!) to make a deep indentation in the center of each cookie.
  4. Bake for about 12 minutes, until set. As soon as the cookies come out of the oven, use a small spoon (or the wine cork again) to reinforce the well in the center of each cookie. Let the cookies cool for about 5 minutes, then transfer to a wire rack to cool completely before filling.

For the filling:

  1. Add the chocolate chips and peanut butter to a small microwave-safe bowl. Microwave in 30 second intervals, stirring after each, until the mixture is smooth. Spoon some of the filling into the center of each cooled cookie. Top immediately with a sprinkle of sea salt. Let the cookies stand until the chocolate is set!


Be sure to melt the coconut oil first and then measure out the correct amount.

Prep time includes 45 minutes for the dough to chill in the fridge. Hands on time is only about 20 minutes.

See the tips & tricks section in the post above for additional notes on the recipe!

Nutrition Information:
Yield: 18 Serving Size: 1
Amount Per Serving: Calories: 96 Total Fat: 7g Saturated Fat: 4g Trans Fat: 0g Unsaturated Fat: 3g Cholesterol: 0mg Sodium: 65mg Carbohydrates: 7g Fiber: 1g Sugar: 5g Protein: 2g
Nutrition data shown is an estimate provided by an online calculator and is for informational purposes only. It should not be considered a substitute for a medical professional’s advice.