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A plate of vegan thumbprint cookies

Vegan Apple Butter Thumbprint Cookies

  • Author: Liz Madsen
  • Total Time: 1 hour
  • Yield: 30 cookies 1x
  • Diet: Vegan


These slightly crispy, slightly soft Vegan Apple Butter Thumbprint Cookies are a quick, tasty dessert. A classic with a delicious fall twist!


  • 1+3/4 cup all purpose flour (see note 1)
  • 1/2 tsp baking powder
  • 1/2 tsp salt
  • 1/2 cup + 1/2 tbsp coconut cream or vegan butter (see note 2)
  • 1/2 cup sugar (see note 3)
  • 1 flax egg (1 tbsp ground flaxseed + 3 tbsp water)
  • 1+1/4 tsp vanilla extract
  • 1/4 cup-ish apple butter or jam


  1. Prep flax egg first.
  2. Mix wet then dry: Mix your sugar and room temp coconut cream or vegan butter in a large bowl. I don’t bother using a mixer for this dough but you can if you want. Add flax egg and vanilla and stir. Then add HALF of the flour and all of the baking powder and salt. Mix until most of it has been incorporated, then add the rest of the flour and mix until well combined.
  3. Chill: Cover the dough and freeze for 20-30 minutes or refrigerate for around 40 minutes to an hour. It will firm up nicely and make it much easier to work with.
  4. Preheat: Preheat your oven to 350 degrees Fahrenheit (or 177 degrees Celsius).
  5. Scoop: Using a small cookie scoop (about 1.5 tablespoon), portion the dough out on parchment or silicone mat lined baking sheets. Keep a few inches between each dough ball--I was able to fit 15 per half-sheet sized baking pan.
  6. Roll: Roll each ball between your hands for a second to smooth it out.
  7. Press: Press a thumb or other finger into each ball, creating a well in the center. If dough is sticking to your fingers, wet your finger between every few cookies. Don’t worry about what it will do to the dough--mine wasn’t really affected by this. Before filling with the apple butter, prep the other sheet of cookies to this point first, since the dough gets a little trickier to work with as it comes to room temperature.
  8. Fill: Use a small or narrow spoon to scoop the filling into the center of each cookie, about half a teaspoon, give or take. Don’t overload them.
  9. Optional: Mix together a little sugar and cinnamon and sprinkle it over each raw cookie. You could also do this before you fill them but I didn’t think of it till after I filled them, to be honest. It worked perfectly and gave the cookies a lovely flavor and texture.
  10. Bake: Bake for approximately 14 - 16 minutes. Mine took about 15 minutes, but I like mine a little crispy on the bottom. Note that they will not be perfectly firm to the touch when they’re still hot, but will firm up more as they cool.You’ll only have to wait about 10 minutes since they’re so little anyway. Enjoy!
  11. Store: Store in an airtight container up to 5 days or freeze in a freezer safe container up to 3 months.


  • Note 1: You can use whole wheat or spelt flour for this recipe, but it may require a touch more moisture. To make this recipe gluten-free, I recommend using a cup for cup GF flour like King Arthur Measure for Measure Gluten-Free Flour or Bob’s Red Mill 1:1 Gluten-Free Flour. I’ve baked with both of these before with good results.
  • Note 2: I bake with coconut cream (thick part of canned coconut milk, but it’s also sold as canned coconut cream) instead of vegan butter, but vegan butter will work. If looking to make these lower fat, I’d try canned pumpkin (um, YUM pumpkin and apple!), mashed banana, or maybe applesauce, though you’ll need to play around with the amounts slightly to make sure you have a thick dough that’s not top sticky.
  • Note 3: I used organic cane sugar in this recipe to achieve the somewhat crispy but chewy texture in the cookie. Other sugars may change the texture, but they should work. Try coconut sugar if looking for an unrefined version. If you want to omit the sugar completely, I’d use a touch more flour until your dough is not sticky.
  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Category: Dessert, Snack
  • Method: Baking
  • Cuisine: American

Keywords: Vegan, Oil-Free, Nut-Free, Soy-Free, Can Be Gluten-Free, vegan thumbprint cookies