Sourdough Thumbprint Cookies Recipe (with Discard)

Thumbprint cookies are one of many classic holiday cookies. These buttery shortbread cookies are pressed in the center with your thumb to create a small indent that is perfect to hold your favorite jam. I wanted to create a recipe for sourdough thumbprint cookies using sourdough discard to create a perfect variation of the classic cookie. 

Two sourdough thumbprint cookies on a white surface with a plate full of the cookies in the background.

What Makes These Cookies Special?

These jam thumbprint cookies are made with sourdough starter discard. I have been on a cookie kick lately and love making sourdough cookies because they are a great way to use up extra sourdough discard (If you need more cookie ideas I have lots of others like my sourdough brown butter chocolate chip cookies, my sourdough ginger molasses cookies, and my sourdough snickerdoodles).

These buttery thumbprint cookies are similar to shortbread. They have an extra crunch from chopped pecans that pairs nicely with raspberry or strawberry jam which sits beautifully at the center of each cookie. 

After much research, I tried several different techniques to make the best thumbprints and I am excited to share the results. 


Here’s what you need to make these sourdough jam thumbprints:

  • Measuring cups and spoons
  • Stand mixer or large bowl with a hand mixer
  • Rubber spatula or wooden spoon
  • A large cookie tray
  • Parchment paper (optional)
  • Wire cooling rack


Sourdough thumbprints ingredients in individual measuring bowls and spoons.

Butter: I use unsalted butter for this recipe but if you have salted, just reduce the salt by 1/2 a teaspoon. 

Sugar: We use plain white sugar for this recipe. I haven’t tried making them with brown sugar but I bet it would be good. I chose not to use brown sugar because it has more moisture which we don’t want a lot of in shortbread cookies.

Egg: we only use the egg yolk for this recipe. You can save the egg white and make scrambled eggs. 

Sourdough discard: You can use active sourdough starter or sourdough discard for this recipe. I recommend using a 100% hydration sourdough discard (equal parts flour and water). If yours has a higher proportion of water, use a little less and add a bit of flour. 

Vanilla extract

All purpose flour: If you want to mix in some whole wheat flour I recommend whole wheat pastry flour and substituting no more than half of the white flour for whole wheat. 


Jam: You can use whatever kind of jam you like but make sure it is jam or fruit preserves and not jelly. Jelly has too much moisture and will soften the cookies too much. I used raspberry jam for mine. 

Pecans: You want to make sure you chop your pecans pretty small so they distribute well in these cookies. If you don’t have pecans or cannot eat them, you can either leave them out or substitute walnuts or almonds.

How to Make Sourdough Thumbprint Cookies

What I love about these cookies is that you can make them in one bowl. Use either a large mixing bowl with a hand mixer, or in the bowl of a stand mixer. 

Preheat the oven to 375F. 

Steps for making sourdough thumbprints. The top left image has the creamed butter and sugar in the bowl of a stand mixer with the paddle attachment. The top right shows the wet ingredients being mixed in that same mixer. The bottom left shows the fully mixed dough with the dry ingredients and pecans. The bottom right shows a thumb making an imprint into each individually portioned cookie dough ball.

Place the butter and sugar in the bowl of a stand mixer and use the paddle attachment to cream together the sugar and butter. 

Add the egg yolk, the sourdough starter or discard, the salt, and the vanilla and continue to mix until well combined. 

On low speed, slowly pour in the flour and the pecans and mix until it is just fully combined and pulling away from the sides of the bowl. 

Use a cookie scoop or a 1 tablespoon measuring spoon to make approximate 1 inch sized balls of dough and place about 2 inches apart on a large baking sheet lined with parchment paper. 

Use your thumb or the back of a 1/2 teaspoon to make a small indent on each cookie dough ball.

Fill each cookie with 1/2 teaspoon (or more if you desire) of jam. If the jam is hard to work with, place it in a small bowl and microwave for 10-15 seconds. This will soften it slightly and make it easier to spoon neatly into the wells. 

12 sourdough thumbprint dough balls with imprints on the top that are being filled with raspberry jam using a small spoon.

Bake the cookies for 18-20 minutes. The edges of the cookies should be slightly golden when done. 

Allow to cool completely before serving on a wire rack or directly on the baking tray. 

Testing Results

I tested several different techniques with these cookies because there are so many different ways that people make thumbprints. 

  • I tried making the indent (thumbprint) at two different times when I was developing this recipe: both at the beginning and halfway through. The cookie that was pressed halfway through formed several cracks around the edges but the one pressed at the beginning held its shape without cracking quite well.  
  • I tried filling the cookies with jam both at the beginning, halfway through baking, and at the end.
    • The cookies with the jam filled at the end did not set well and were more messy because the jam moved around easily. These cookies did look slightly nicer though, because the jam was a bit more shiny than the cookies with the baked jam. 

The cookies with jam filled halfway through produced similar results to those with jam added at the beginning. These cookies had jam that was nicely set and didn’t move around much. I was even able to stack these cookies without the jam transferring very much. Because these two groups had similar results, I decided that adding the jam at the beginning was the simplest method with the best results. 

Several sourdough thumbprint cookies on a white surface with a plate full of the cookies in the background. There is also a small bowl filled with jam and a small spoon.

Can You Freeze Sourdough Thumbprints?

You can freeze these cookies but I recommend waiting to fill them jam until you are ready to serve them. This means you would bake the cookies before filling them if you are planing to freeze them. The reason is that the jam will release more liquid when they defrost, resulting in a soggy cookie. 

You can also freeze the dough ahead of baking. Place the dough in an airtight gallon freezer bag and defrost in the fridge the day before you plan to make them. 

 Alternatively, you can roll out the cookie dough balls with the imprint and freeze them. This will make them easier to just place on the cookie sheet and bake when you are ready to make them. 

How to Store

Store on an a plate wrapped in plastic wrap or in an airtight container. There are no standardized guidelines in place for how long you can keep thumbprint cookies. A common concern is whether it is safe to store these cookies at room temperature because of the jam. Most recipes out there recommend leaving thumbprint cookies in an airtight container at room temperature for up to one week. 

My thoughts are that placing the jam on the cookies before baking reduces some of the safety risks because it reduces the moisture and cooks the jam. That being said, I still recommend only leaving these cookies at room temperature for up to three days. If you need to store them for longer, I recommend keeping them in the fridge, just to be safe. 

I hope you enjoy these sourdough discard thumbprint cookies. You can also check out these sourdough recipes:

My Easy Flaky Sourdough Pie Crust

Decadent and Delicious Sourdough Brownies

For more sourdough discard recipes I encourage you to join my email list. There you will get all the updates for my new recipes plus other updates and exclusive content. Until next time, happy baking!

Two sourdough thumbprint cookies on a white surface with a plate full of the cookies in the background.

Sourdough Thumbprint Cookies

These sourdough thumbprint cookies are a buttery shortbread cookie filled with your favorite jam. They are easy to make and sure to be a hit during the holidays.
Prep Time 20 minutes
Cook Time 18 minutes
Total Time 38 minutes
Course Dessert
Cuisine American
Servings 40 cookies
Calories 100 kcal


  • 1 Stand mixer or large bowl with hand mixer
  • Measuring cups and spoons
  • rubber spatula or wooden spoon
  • 1 large cookie sheet
  • Parchment Paper optional
  • Wire cooling rack


  • 1 cup unsalted butter 2 sticks
  • cup sugar
  • 1 egg yolk
  • cup sourdough discard
  • 1 teaspoon vanilla extract
  • 1 teaspoon salt
  • cup all purpose flour
  • cup jam such as raspberry, strawberry or apricot
  • ½ cup chopped pecans optional


  • Preheat oven to 375℉.
  • In the bowl of a stand mixer, cream together the butter and sugar on medium speed.
  • Add the egg yolk, sourdough discard, vanilla, and salt and mix until well combined.
  • Slowly add the flour and pecans on low speed until just fully combined.
  • Scoop the cookie dough into approximate 1 tablespoon (about 1 inch) cookie dough balls.
  • Place each cookie dough ball on a large baking sheet lined with parchment paper approximately 2 inches apart.
  • Use your thumb or the back of a small spoon to make an indent in the top of each cookie.
  • Use a small spoon to fill each indent with approximately ½ teaspoon (or more if you desire) of jam. If the jam is hard to work with, place it in a small bowl and microwave for 10-15 seconds to soften it.
  • Bake the cookies for 18-20 minutes or until the edges appear slightly golden.
  • Allow to cool completely before serving.


Serving: 1cookieCalories: 100kcalCarbohydrates: 11gProtein: 1gFat: 6gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 0.2gCholesterol: 17mgSodium: 60mgPotassium: 18mgFiber: 0.4gSugar: 5gVitamin A: 149IUVitamin C: 0.3mgCalcium: 5mgIron: 0.4mg
Keyword Cookies, Sourdough, Sourdough Discard
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