Vegan thumbprint cookies make a wonderful holiday cookie with their easy preparation and minimal ingredients.

A soft, buttery and chewy almond flour cookie is coated in crunchy chopped pecans, flavored with vanilla and almond extracts, then filled with your favorite jam.

You won’t be able to resist these gluten-free and vegan thumbprint cookies!

Vegan thumbprint cookie recipe on a plate.
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If you put me in front of a whole table of holiday cookies and I could only choose one, it’d be a thumbprint cookie, no contest.

They’re the perfect balance of everything I want in a cookie – a soft buttery base that melts in your mouth with a lovely contrast from the jammy fruit center.

And if that wasn’t enough, they’re often made with a touch of almond extract which also just happens to be my absolute favorite flavor in cookies and pastries.

Hence my love of pignoli cookies and why I love these pumpkin biscotti so much too. Just that hint of almond from 1/2 teaspoon of extract is everything!

Thumbprints are like the pie of the cookie world and considering I’d take pie (or a sour cherry crisp) over cake any day, it’s no surprise these cute little cookies steal my heart.

This season, I wanted to create the perfect vegan thumbprint cookie.

It’s a simple cookie.

One that requires just a handful of ingredients and a quick and easy prep. But don’t let that fool you into thinking it’s not worthy of a spot in your holiday baking rotation.

These vegan thumbprints consistently turn out splendidly with their melt in your mouth texture (the dough is dreamy!), delicious almond paste type of flavor and bright fruity center.

They’re stunning on a plate and even better in your mouth!

Vegan thumbprint cookie dough in a bowl with spatula.


While almost all the thumbprint cookie recipes I’ve made are actually vegan, I wanted to create a classic one this time around.

These almond pulp thumbprint cookies, while egg and dairy-free, use leftover almond pulp from making almond milk and I realize that’s not quite accessible for everyone.

Then there’s these tart cherry fudge thumbprints, also vegan but they use black beans in the cookie dough.

Don’t hate on that by the way, black beans make excellent baked goods! These vegan black bean brownies are a favorite!

And, I also have these almond chocolate thumbprint cookies. They’re an OG recipe I created back in the paleo days but use egg whites.

So, while there’s plenty to choose from in the thumbprint world, these vegan thumbprints are what will become your go-to recipe.

Rolling vegan thumbprint cookie dough balls in chopped pecans.


  • almond flour
  • coconut flour
  • salt
  • baking powder
  • melted coconut oil
  • maple syrup
  • apple cider vinegar
  • vanilla and almond extract
  • jam of choice
  • chopped pecans (optional for rolling the outside of the thumbprints)

With 2 cups of almond flour and just 1 tablespoon of coconut flour these are primarily an almond flour thumbprint cookie.

The small amount of coconut flour just helps absorb some of the oils from the almond flour and firm up the dough a bit.

It can be omitted if you don’t have it on hand but I find it does help with the “greasy” feeling of an all nut flour dough.

Making "thumbprint" in vegan thumbprints on baking sheet.


Start by preheating the oven to 350°F. Line a large baking sheet with either parchment paper or a silicone baking mat.

If using the chopped pecans for the outside of the cookies, place them in a small shallow bowl or plate.

Combine all the other ingredients for the cookies except for the jam in a medium sized mixing bowl.

Stir until well combined and the dough is homogenous in texture.

Roll the dough into balls, I like to use a small cookie scoop for this.

Roll the ball of dough around in the pecans until the outside is coated. Skip this step if not using the nuts.

Place the dough ball on the baking sheet and repeat with remaining dough.

Using your thumb, gently press down in the center of each ball to create an indent for the jam. Small cracks around the side are fine. You can pinch together any larger cracks that form if desired.

Spoon the jam of your choice into the indentation of each cookie.

Bake the thumbprints for 11-13 minutes until the edges of the cookie (or nut coating) start to turn just barely golden brown.

Remove the baking sheet from the oven and let rest for 10 minutes before transferring the cookies to a cooling rack.

The thumbprints will be soft straight out of the oven but will firm up as they cool.

Filling vegan gluten-free thumbprint cookies with jam.


Almond Flour – For the buttery, smooth, melt-in-your-mouth type of texture, it’s best to bake with super fine blanched almond flour. Bob’s Red Mill makes a good one that’s usually easily found in stores.

Thumbprints are forgiving though and you can certainly use almond meal they’ll just be a bit “heartier” in texture.

Jam – Any type of jam can be used to fill a thumbprint cookie.

I chose raspberry jam for these but I also love thumbprints with apricot jam or orange marmalade. Some homemade cranberry sauce would also be delicious and festive.

Or, try some persimmon jam for a wonderful seasonal option too!

Chopped Nut Coating – I love the contrast in texture of rolling the thumbprints in some chopped pecans. This is totally optional though if you prefer a smooth cookie.

Chopped almonds, hazelnuts or walnuts can also be used in place of pecans if preferred.

Extracts – Don’t skip out on the almond extract in these cookies!

Combined with the almond flour, the almond extract creates a wonderful marzipan-like flavor that’s irresistible.

Baked almond flour thumbprint cookies with raspberry jam on a baking sheet.


The best way to store thumbprint cookies is actually loosely covered on the counter for up to 5-7 days.

If stored in an air-tight container they tend to soften up too much.

The thumbprints are freezer friendly too!

If freezing the cookies, make sure they’ve completely cooled from the oven then place them in a container with wax paper between each layer of cookies so they don’t stick together.

They’ll keep in the freezer for up to a couple of months and can be thawed and enjoyed as desired.

Plate of almond flour vegan thumbprint cookies with raspberry jam.


If you’d like to prepare the cookie dough for these vegan thumbprints in advance and bake them later, you can.

Prepare the dough in the bowl as directed. Cover and chill until ready to roll out and bake.

This can be done up to 2 days in advance of baking.

Chilling the dough is another good option if you find it to be a little too greasy or soft when handling. A quick chill of 15-20 minutes can help when rolling out into balls.

I don’t find this step necessary but it can be utilized if needed.

Shortbread cookies are also a great option for prepping ahead. These matcha shortbread cookies are a fun festive option for the holidays too!

Pecan crusted vegan thumbprint cookies stacked on a table surface.


Almond flour is one of the best ingredients for gluten-free baking.

Having had thumbprints made with both regular wheat flour and those with an almond flour base, I actually prefer the almond flour cookies.

The nuttiness and natural oils in almond flour create a much more tender thumbprint.

And, the flour serves as both a gluten-free option as well as eliminating the need for copious amounts of butter in the recipe.

It’s a win-win because the cookies are suitable for those that eat a gluten-free and vegan diet without compromising at all in taste or texture for those that don’t!

Vegan gluten-free thumbprint cookies with raspberry jam and chopped pecans.

I hope these easy vegan thumbprints make their way into your kitchen this holiday season (or any time of year for that matter because they’re definitely not just a holiday cookie!).

They’re a classic for good reason – a consistently delicious and simple cookie that everyone seems to love!

And with some easy tweaks, they’re now suitable for vegans and gluten-free eaters alike.

Looking for another classic dessert with a vegan twist? Try this vegan coconut cream pie or make some vegan oatmeal raisin cookies.


Gluten-free vegan oatmeal chocolate chip cookies
Paleo blueberry thumbprints
Sweet potato cookies
Chocolate chip chickpea blondies
Healthy cookie dough bites

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4.45 from 9 votes

Vegan Thumbprint Cookies

Servings: 15 cookies
Prep: 15 minutes
Cook: 12 minutes
Total: 27 minutes
Vegan thumbprint cookies.
Vegan thumbprint cookies combine a sweet buttery cookie base with chopped pecans and a sweet jam filling. An irresistible addition to your holiday baking!


  • 1/3 cup pecans, finely chopped
  • 2 cups almond flour
  • 1 tablespoon coconut flour
  • 1/4 teaspoon salt
  • 1/4 teaspoon baking powder
  • 1/4 cup melted coconut oil
  • 1/4 cup maple syrup
  • 1 teaspoon apple cider vinegar
  • 1 teaspoon vanilla extract
  • 1 teaspoon almond extract
  • about 1/3 cup jam of choice


  • Preheat oven to 350°F. Line a baking sheet with a silicone mat or parchment paper.
  • Place chopped pecans in a shallow bowl or small dish, set aside.
  • Combine all ingredients except jam in a bowl and mix until a dough forms.
  • Form dough into balls then roll in pecans. Place on baking sheet and gently press down in the center using your thumb to create an indent. Pinch together any large cracks around the outside.
  • Spoon jam into the center of each cookie.
  • Bake for 11-13 minutes until edges start to brown just slightly. Remove cookies from the oven and let rest on the baking sheet until cooled. The thumbprints will be soft at first but crisp up as they cool.


Serving: 1COOKIECalories: 173kcalCarbohydrates: 12gProtein: 4gFat: 13gSaturated Fat: 4gPolyunsaturated Fat: 8gSodium: 47mgFiber: 2gSugar: 8g

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American
Founder and Writer at Running to the Kitchen | About

Gina Matsoukas is an AP syndicated writer. She is the founder, photographer and recipe developer of Running to the Kitchen — a food website focused on providing healthy, wholesome recipes using fresh and seasonal ingredients. Her work has been featured in numerous media outlets both digital and print, including MSN, Huffington post, Buzzfeed, Women’s Health and Food Network.

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Recipe Rating


  1. 2 stars
    i had to basically alternate/tweak every other ingredient in this recipe or else it would have likely came out superr dry & nasty ..turned out tasty after my (tweaking)

  2. I love these cookies and they are very popular when I made them for a gathering. I’d like to make a chocolate version with cocoa powder. Have you tried that?

  3. I wish I could give this Vegan thumbprint cookies recipe more than the 5-stars I gave on the review! So flavorful and good, we put them on the list for Christmas Eve.