Cookies that are easy and healthy, with a delicious nutty flavor complemented by sweet jam. These Healthy Thumbprint Cookies are low sugar and low fat, and free of dairy and eggs.
They're made with a combination of whole wheat pastry flour and almond flour to keep the cookie moist and light with tons of flavor!

In addition to being heart healthy, these thumbprint cookies are vegan, as we're not using eggs, milk, butter, or any other animal products.
These healthy cookies are great for Christmas, Easter, or really just because. They are low fat, low sugar, and low sodium, making them a perfect end to any meal.
You may wish to learn more about how to cook with less salt.
Ingredients
The base of our thumbprint cookies is a blend of almond flour and whole wheat pastry flour. Do not try to substitute whole wheat flour. Your cookies will turn out very dense.

- Whole wheat pastry flour
- Almond flour
- Salt
- Unsweetened applesauce
- 100% pure maple syrup
- Grapeseed oil
- Vanilla extract
- No added sugar fruit jam
See recipe card for quantities.
Instructions
These healthy thumbprint cookies are prepared almost the same as regular thumbprint cookies.

Combine all the dry ingredients in a large bowl and mix.

In a separate bowl, combine all the wet ingredient and mix.

Pour the wet ingredients into the dry ingredients.

Mix well, until a thick dough forms.

Form balls with one tablespoon of dough each.

Use a the back of a teaspoon (or your thumb) to press wells into the balls of dough, being careful they don't crack apart.

Fill each well with jam.

Bake until the cookies just start to brown and no more.
Hint: if the dough cracks apart too much when you are forming the indentation, the jam will leak out as it bakes. Make sure to firmly press the dough together as you roll the balls.
Substitutions
Try some of these substitutions if you need a modification:
- Flour - to make these gluten free, use an all purpose gluten free flour instead of the whole wheat pastry flour. It will no longer be whole grain unless your gluten free flour is whole grain.
- Oil - use sunflower, peanut or canola oil instead of grapeseed. A neutral oil will be best, which is why I'm not recommending olive oil for this particular recipe.
- Sweetener - use either white or brown sugar in place of maple syrup. Honey does not work well in this recipe.
- Nut free - to make this nut free, use ½ cup finely ground sunflower seeds instead of almond flour, or simply use an extra ½ cup whole wheat pastry flour.
Variations
Here are several ideas on how to mix up this recipe for a little variety!
- Walnuts - use finely ground walnuts (or any finely ground nut) in place of almond flour
- Jam - I use strawberry jam, but blueberry, cherry, or even orange marmalade would work great (learn more about choosing a healthy jelly)
- Applesauce - try a flavored unsweetened applesauce for extra flavor, like strawberry or blueberry. You can even use a mashed banana instead if you like.
You might also really like these Peanut Butter and Jelly Dessert Bars.
Storage
Almond flour thumbprint cookies will store great in an airtight container at room temperature for about 5 days. You might get a few more days out of them if it's not hot and humid.
These can be frozen for up to six months. Thaw at room temperature for an hour or two.
Top tip
Absolutely use whole wheat pastry flour for this and other baked goods. If you try to use regular whole wheat flour, your cookies will be hard and dense.
FAQ
No. This particular recipe will not turn out if you use all almond flour.
This can happen for two reasons. Either the dough it too dry, or you are trying to indent them too fast or too deeply.
Try pressing down more slowly, and not as deep first. If that doesn't work, you can try remixing the dough with a few teaspoons of water and trying again.
Related
Looking for other recipes like this? Try these:
You must use the category name, not a URL, in the category field.Pairing
These are my favorite dishes to serve with Healthy Thumbprint Cookies:
📖 Recipe

Healthy Thumbprint Cookies
Ingredients
- 1 ½ cup Whole Wheat Pastry Flour
- ½ cup Almond Flour
- ⅛ teaspoon Salt
- ¼ cup Unsweetened Applesauce
- ¼ cup 100% Pure Maple Syrup
- 2 tablespoon Grapeseed Oil
- 1 teaspoon Vanilla Extract
- ⅓ cup No Added Sugar Fruit Jam
Instructions
- Preheat oven to 350° F.
- In a large bowl, mix together the whole wheat pastry flour, almond flour, and salt.
- In a separate bowl, mix the applesauce, maple syrup, oil, and vanilla.
- Pour the wet mixture into the dry ingredients, and mix thoroughly.
- Measure out the dough, 1 tablespoon at a time, and roll it into a ball.
- Place the balls on a lined baking sheet, about 2 inches apart. You will probably need two baking sheets, or will have to do two batches.
- Now use the back of a teaspoon (or your thumb) to gently press a hole into each ball. It’s ok if they crack a little.
- Fill each hole with no added sugar jam.
- Bake 12-15 minutes, until the cookies are just starting to brown.
- Cool on the baking sheet for 5 minutes before moving to a cooling rack to cool completely.
Nutrition
*Nutrition information is an estimate, and will change based on the brand and individual ingredients and amounts you use. This is provided for your convenience only.
Jean says
What could I use instead of the grapeseed oil?
Laura Yautz says
Hi Jean, you can use any oil you like, but I recommend one more neutral in flavor, like avocado or canola oil. Olive oil would work, but you may taste it - you may or may not enjoy that in a cookie 🙂 Hope this helps! Happy baking!