Healthy Carrot Cake Thumbprint Cookies
Yields: 24 bite-sized cookies
These fun bite-sized cookies literally taste just like carrot cake! They have the same supremely soft and moist texture, and they also have lots of carrots, rich spice flavor, and sweet centers that taste like velvety smooth cream cheese frosting. They’re perfect for Easter — or any day you’re craving carrot cake! Leftovers will keep for at least one week if stored in an airtight container in the refrigerator.
  • for the cookies
  • 1 cup (120g) white whole wheat flour or gluten-free* flour (measured like this)
  • ¾ tsp baking powder
  • ¾ tsp ground cinnamon
  • ¼ tsp ground allspice
  • ¼ tsp ground nutmeg
  • ¼ tsp salt
  • 1 ½ tbsp (21g) unsalted butter or coconut oil, melted and cooled slightly
  • 1 large egg white, room temperature
  • 1 ½ tsp vanilla extract
  • 1 tsp nonfat milk, room temperature
  • ½ cup (96g) coconut sugar
  • ½ cup (53g) finely grated carrots (about one medium, peeled first — and see Notes!)
  • for the filling
  • 2 tbsp (30g) plain nonfat Greek yogurt
  • 2 tbsp (28g) well-softened light cream cheese (see Notes!)
  • ¼ tsp liquid stevia, or adjusted to taste
  • ⅛ tsp vanilla extract
  1. To prepare the cookies, whisk together the flour, baking powder, cinnamon, allspice, nutmeg, and salt in a medium bowl. In a separate bowl, whisk together the butter, egg white, vanilla, and milk. Stir in the coconut sugar. Add in the flour mixture, stirring until incorporated. Fold in the carrots. Chill the cookie dough for 30 minutes.
  2. To prepare the filling, mix together the Greek yogurt, cream cheese, stevia, and vanilla in a small bowl until completely smooth. Transfer the mixture into a zip-topped bag.
  3. Preheat the oven to 350°F, and line a baking sheet with a silicone baking mat or parchment paper.
  4. {See Notes below before beginning this step!} Roll the cookie dough into 24 small spheres, and place them on the prepared baking sheet. Using your index finger or thumb, make an indentation in the center of each. Cut off a small piece of the corner of the filling bag, and pipe it into the indentations. Bake at 350°F for 9-11 minutes. Cool on the baking sheet for 10 minutes before carefully transferring to a wire rack. (If the cookies stick to the baking sheet, slide a knife underneath each cookie first!)
Notes: This cookie dough is sticky, and that’s intentional! It gives these cookies the same texture as carrot cake. However, that means the cookie dough will stick to your bare hands. So in Step 4, moisten your fingers and palms with water before rolling the cookie dough into spheres and making indentation in the centers. (I keep a small bowl of water next to the baking sheet, and I re-moisten my hands in between shaping each cookie. The cookie dough never sticks when I do that!)

For the gluten-free flour, use as follows: ¼ cup (30g) millet flour, ¼ cup (30g) tapioca flour, 3 tablespoons (21g) coconut flour, and ¾ teaspoon xanthan gum. Most store-bought gluten-free flour blends (like this one!) will work as well, if measured like this.

Whole wheat pastry flour, regular whole wheat flour, or all-purpose flour may be substituted for the white whole wheat flour.

It’s important to measure the flour correctly, using this method or a kitchen scale. (← That’s the one I own and love!) Too much flour will make your cookies turn out dry and crumbly, rather than soft and chewy. If you can’t incorporate all of the flour into your cookie dough, then stir in additional milk ½ teaspoon at a time until all of the dry ingredients are incorporated.

For a stronger spice flavor, increase the cinnamon to 1 teaspoon. (That’s the way I prefer my cookies!)

Any milk may be substituted for the nonfat milk.

Brown sugar may be substituted for the coconut sugar.

Do NOT substitute store-bought pre-shredded carrots (also called matchstick carrots). They’re thicker and drier, and they don’t soften properly while baking. Use the finest holes of a box grater to grate your carrots. This tiny size ensures the carrots completely soften while baking, which ensures your cookies turn out perfectly soft and chewy.

Any type of cream cheese will work (Neufchâtel cream cheese, Greek yogurt cream cheese, fat-free cream cheese, even regular cream cheese!). Just make sure it’s very well softened first!

I highly recommend using the liquid stevia! It’s one of my favorite ingredients, and you’ll use it in all of these recipes of mine too. (I buy mine online here because it’s the cheapest price I’ve found!) However, if you prefer, 1 ½ tablespoons of powdered sugar, granulated sugar, brown sugar, or coconut sugar may be substituted in the filling. I don’t recommend using honey, maple syrup, or agave because it’ll make the filling too liquidy.

This recipe is easily doubled!

{gluten-free, clean eating, low fat}
Recipe by Amy's Healthy Baking at