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.

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 ½ tablespoon measure (round). Fill the indentation with jam and bake. Ta da!

Here is a handy dandy printable!

Whole Wheat Thumbprint Cookies
Ingredients
- ¾ cup unsalted butter, at room temperature 1 ½ sticks
- ¼ cup sugar
- ¼ cup light brown sugar See notes
- ½ teaspoon pure vanilla extract
- 1 ¾ cups whole wheat pastry flour See notes
- ¼ teaspoon salt
- Raspberry and/or apricot jam See notes
Instructions
- Plan ahead - Take butter out of the refrigerator and keep in mind that the dough has to be chilled for 30 minutes.
- Preheat your oven to 350 degrees F/175 degrees C.
- 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.
- In a separate mixing bowl, sift together the flour and salt.
- With the mixer running on low speed, add the flour mixture to the creamed butter and sugar.
- Mix until the dough comes together. you can add upto a tablespoon of milk if need be.
- 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.
- 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.
- Place the balls on an ungreased cookie sheet and press a light indentation into the top of each using a round ½ tablespoon measure (see tools used below). Drop ¼ teaspoon of your choice of jam into each indentation.
- Bake for 20 to 25 minutes, until the cookies are golden brown. Cool for 10 minutes and serve.
Notes

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.
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Tools Used:
Stand Mixer: Sieve:
Mixing Bowl:
Measuring Cups:
Measuring Spoons:
Cookie Sheet:
Mrs Type A
Wow, looks amazing! I had no idea whole wheat flour could lead to such great results! I'm doing something wrong!
Adharsh
Mouthwatering article .... Really gonna suggest to my friends and my mom... Thanks for it and keep going
Tracy Albiero
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.
Mohamed Jamoza
I'll be sure to share this with my wife, but only after trying it myself to surprise her. Thanks a lot for this.
Vaishali
Thanks, That's a great idea!
Rupal Srivastava
These cookies are so mouth watering and easy to make.
Vaishali
Thanks Rupal. Easy to make for sure!
Monidipa Dutta
As usual i love the food so I loved the recipe. Pinning it in good food.
Jolie Starrett
Nice variation on the thumbprint cookie!
Hackytips
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 🙂
The Honest Reader
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.
Elease
These look amazing! Raspberry jam is my all time fave. Is this recipe similar to a Linzer tart?
Vaishali
Thanks Elease. I'm afraid I don't know about Linzer tart. Might have to look that up..:P
Carla
I think what characterizes a Linzer tart or cookie is the ground up nuts in the flour, not just the raspberry jam filling.
Vaishali
Thanks, Carla and good point!
Aashirvad Kumar
That’s pretty cool. The guide has manythings which are really awesome for the peoples. Their many things are mentioned which are useful.
Erica
These sound so yummy! I’m definitely going to try making them. I’m always looking for new cookie recipes.
Vaishali
Thanks Erica. Please let me know if you try them..:)