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Whole Wheat Thumbprint Cookies

A healthier take on a Christmas classic! These whole wheat thumbprint cookies, with a buttery shortbread base and warm jam center, are an ultimate indulgence.

I have been on a cookie baking spree past few days so much so that I feel like I am obsessed with it. My mind actually feels like cookie dough..ha ha – soft an mushy! In the years gone by, I have made sugar cookies (recipe here), chocolate chip cookies and last year I added these nut free carrot cake cookies to the holiday cookie baking tradition. I wanted to try some new recipes this year – some from the memory lanes of my childhood and some favorites. Also, a major focus this year is to keep the treats as healthy as possible. So, I start this season of holiday cookie baking with these whole wheat thumbprint cookies.

Classic Jam-filled thumbpring cookies made healthier with whole wheat flour
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There is something about jam and cookies that takes me back to my years in the town where I grew up. A small township tucked in the plains, between the border lines of India and Pakistan. There was nothing fancy about our town. No big shopping stores and not many restaurants. I do clearly remember two little bakeries in town that made the best cookies and bread. My dad would alternate between the two to bring us treats whenever he was visiting the bazaars. These whole wheat thumbprint cookies, filled with jam recipe is based on one of the many different kinds of cookies from one of the bakeries in our sweet little town.

Recipe Run Down

Though the thumbprint cookies that I grew up eating were not whole wheat, but these are. I am going to convince myself that these are healthier than the regular thumbprints so that I can have an extra one. Whole wheat flour adds a nice nuttiness to the cookie and I feel it adds a little more texture too. These whole wheat thumbprint cookies are shortbread cookies of sorts. Shortbread cookies do not contain a leavening agent so are denser than their counterparts for example a sugar cookie. These tend to be denser and have bite to them. Which I love!
Recipe of a shortbread cookie normally consists of three parts flour, one part sugar and two parts butter. Yes, that’s right – two parts butter! There goes my health claim. But we will consider them healthier than the all purpose flour version, shall we?

Plan ahead before you start these whole wheat thumbprint cookies and take the butter out of the refrigerator. We need room temperature butter. You know it is one of my baking rules (hah). Cream together butter and sugar (we will use both white and brown sugar here). Be a good baker and sift together the dry ingredients – whole wheat pastry flour and salt. Mix the dry ingredients with butter-sugar mixture (plus vanilla) until the dough comes together. Form into a disc or a ball, wrap in plastic wrap and chill for at least 30 minutes. Chilling time required.  Roll the dough into 1 tablespoon balls, place them on a cookie sheet and press a light indentation into the top of each with a 1/2 tablespoon measure (round). Fill the indentation with jam and bake. Ta da!

Classic Jam-filled thumbpring cookies made healthier with whole wheat flour

Here is a handy dandy printable!

Classic Jam-filled thumbpring cookies made healthier with whole wheat flour
4.67 from 6 votes

Whole Wheat Thumbprint Cookies

A healthier take on a Christmas classic! These whole wheat thumbprint cookies, with a buttery shortbread base and warm jam center, are an ultimate indulgence. These melt-in-your-mouth, have a tender crumb and are just the right amount of sweet. Everyone will love these perfect jam-filled whole wheat thumbprint cookies!

Course Dessert
Cuisine American
Keyword Whole Wheat Thumbprint Cookies
Prep Time 20 minutes
Cook Time 25 minutes
Chill and Cooling time time 40 minutes
Total Time 45 minutes
Servings 24 cookies
Author Vaishali


  • 3/4 cup unsalted butter, at room temperature 1 1/2 sticks
  • 1/4 cup sugar
  • 1/4 cup light brown sugar See notes
  • 1/2 teaspoon pure vanilla extract
  • 1 3/4 cups whole wheat pastry flour See notes
  • 1/4 teaspoon salt
  • Raspberry and/or apricot jam See notes


  1. Plan ahead – Take butter out of the refrigerator and keep in mind that the dough has to be chilled for 30 minutes.

  2. Preheat your oven to 350 degrees F/175 degrees C.

  3. In your stand mixer fitted with the paddle attachment, cream together the butter and both the sugars until they are light and creamy and then add the vanilla.

  4. In a separate mixing bowl, sift together the flour and salt.

  5. With the mixer running on low speed, add the flour mixture to the creamed butter and sugar.

  6. Mix until the dough comes together. you can add upto a tablespoon of milk if need be.

  7. Cut a piece of plastic wrap big enough to hold the dough and lay it on your kitchen counter. Dump the dough on the plastic wrap and roll together into a flat disk. Wrap in plastic completely and chill for 30 minutes.

  8. After 30 minutes, take the dough out and break about a tablespoon of dough from the disc and roll it into approximately 1 inch balls.

  9. Place the balls on an ungreased cookie sheet and press a light indentation into the top of each using a round 1/2 tablespoon measure (see tools used below). Drop 1/4 teaspoon of your choice of  jam into each indentation.

  10. Bake for 20 to 25 minutes, until the cookies are golden brown. Cool for 10 minutes and serve.

Recipe Notes

If you do not have brown sugar, you can use all regular sugar.

All purpose flour will work instead of the whole wheat pastry flour.

Feel free to choose the jams of your choice. These are just the classics.


Classic Jam-filled thumbpring cookies made healthier with whole wheat flour

The cookies will stay fresh when stored in an air tight jar for up to 10 days (who are you kidding?). Some recipes for thumbprint cookies call to bake the cookie dough before adding the jam, but I like to adding the jam before baking so that it bakes into the dough and becomes nice and bubbly.

I certainly hope that you enjoy eating these cookies as much as I enjoyed bringing this recipe to you and this recipe of Whole Wheat Thumbprint Cookies becomes a new holiday favorite at your house.

Love – Vaishali.

Other recipes you might enjoy

Christmas Sugar Cookies

Nut free Carrot Cake Cookies

Carrot Cake Cookie

Tools Used:

Stand Mixer: Sieve: Mixing Bowl: Measuring Cups: Measuring Spoons: Cookie Sheet:

Stuff you might need:


  1. Mrs Type A

    January 4, 2019 at 10:00 am

    Wow, looks amazing! I had no idea whole wheat flour could lead to such great results! I’m doing something wrong!

  2. Adharsh

    January 4, 2019 at 10:24 am

    5 stars
    Mouthwatering article …. Really gonna suggest to my friends and my mom… Thanks for it and keep going

  3. Tracy Albiero

    January 4, 2019 at 10:52 am

    These remind me of my childhood. My grandma used to make them all the time. I am glad to know there is a wheat version. Might be time to make them with my little girl.

  4. Mohamed Jamoza

    January 4, 2019 at 1:55 pm

    I’ll be sure to share this with my wife, but only after trying it myself to surprise her. Thanks a lot for this.

    1. Vaishali

      January 4, 2019 at 2:17 pm

      Thanks, That’s a great idea!

  5. Rupal Srivastava

    January 4, 2019 at 3:02 pm

    These cookies are so mouth watering and easy to make.

    1. Vaishali

      January 4, 2019 at 3:15 pm

      Thanks Rupal. Easy to make for sure!

  6. Monidipa Dutta

    January 4, 2019 at 4:21 pm

    5 stars
    As usual i love the food so I loved the recipe. Pinning it in good food.

  7. Jolie Starrett

    January 4, 2019 at 6:02 pm

    5 stars
    Nice variation on the thumbprint cookie!

  8. Hackytips

    January 4, 2019 at 6:38 pm

    Looks yum! I like the way you present your recipes, photographs, & the Plugins you use. Whenever it comes to cookies I see recipes dominating Maida (All purpose flour) which is not good for health. These cookies are healthy and delicious. I will try and let you know how it turns out. Thanks Vaishali 🙂

  9. The Honest Reader

    January 5, 2019 at 8:23 am

    3 stars
    Oooo I loved these! My husband and I love making thumbprint cookies together, but I have definitely never seen a whole wheat version! What a good recipe.

  10. Elease

    January 5, 2019 at 11:13 am

    5 stars
    These look amazing! Raspberry jam is my all time fave. Is this recipe similar to a Linzer tart?

    1. Vaishali

      January 8, 2019 at 9:42 am

      Thanks Elease. I’m afraid I don’t know about Linzer tart. Might have to look that up..:P

    2. Carla

      December 16, 2021 at 12:07 pm

      I think what characterizes a Linzer tart or cookie is the ground up nuts in the flour, not just the raspberry jam filling.

      1. Vaishali

        January 2, 2022 at 12:01 am

        Thanks, Carla and good point!

  11. Aashirvad Kumar

    January 7, 2019 at 1:10 am

    5 stars
    That’s pretty cool. The guide has manythings which are really awesome for the peoples. Their many things are mentioned which are useful.

  12. Erica

    January 7, 2019 at 1:12 pm

    These sound so yummy! I’m definitely going to try making them. I’m always looking for new cookie recipes.

    1. Vaishali

      January 7, 2019 at 1:57 pm

      Thanks Erica. Please let me know if you try them..:)

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