Snickerdoodle Thumbprint Cookies with Chocolate

This healthy cinnamon-sugar snickerdoodle thumbprint cookie recipe has an added bonus: chocolate filling! With slightly crispy edges and a chewy, chocolaty center, these snickerdoodle cookies are the ultimate crowd pleaser.

Cook Time:
1 hr 30 mins
Total Time:
1 hr 30 mins
4 dozen 1 1/2-inch cookies
Nutrition Profile:


Chocolate Filling

  • 3 ½ ounces dark chocolate, coarsely chopped

  • ¼ cup whole milk

  • ¼ teaspoon vanilla extract

  • 3 tablespoons confectioners' sugar

Cookie Dough & Cinnamon-Sugar

  • 2 cups all-purpose flour, plus more if needed

  • cup white whole-wheat flour (see Tip)

  • 1 ½ teaspoons baking powder

  • ¼ teaspoon salt

  • cup canola oil or corn oil

  • 4 tablespoons unsalted butter, slightly softened

  • 1/2 cup plus 5 tablespoons granulated sugar, divided

  • 1 large egg

  • Finely grated zest of 1 medium lemon

  • 1/4 cup plus 1 tablespoon honey

  • 2 ½ teaspoons vanilla extract

  • ½ teaspoon almond extract or lemon extract

  • 3 tablespoons ground cinnamon


  1. To prepare chocolate filling: Put chocolate in a small, deep heatproof bowl. Set a fine sieve by the bowl. Put milk in a 2-cup microwave-safe glass measuring cup and microwave on High just until it begins to boil and foam up the sides, 40 to 60 seconds. Pour half the hot milk through the sieve onto the chocolate and let stand without stirring for about 2 minutes to soften the chocolate. Stir vigorously until smooth and the chocolate is mostly melted.

  2. Pour the remaining milk through the sieve into the bowl. Add vanilla. Stir vigorously until smooth. Sift confectioners' sugar onto the mixture and stir in thoroughly. Refrigerate until very cold and stiff.

  3. To prepare cookies: Position a rack in middle of oven; preheat to 350 degrees F. Line a large baking sheet(s) with parchment paper.

  4. Whisk all-purpose flour, whole-wheat flour, baking powder and salt in a medium bowl. Beat oil, butter, 1/2 cup plus 1 tablespoon sugar, egg and lemon zest in a mixing bowl with an electric mixer on low speed until well blended. Beat in honey, vanilla and almond (or lemon) extract until evenly incorporated.

  5. With the mixer on low speed, then medium speed, beat about half the flour mixture into the wet ingredients until incorporated. Beat in the remaining flour mixture until just incorporated.

  6. Divide the dough into quarters. Roll each quarter into a 9-inch "log." Slice the log into 12 equal pieces. Roll each piece into a ball.

  7. Combine the remaining 4 tablespoons sugar with cinnamon in a small bowl and transfer to a plate. Roll each ball in the cinnamon-sugar. Place about 1 1/2 inches apart on a prepared baking sheet. Press a well into the center of each cookie with a thumb. Fill with about 1/2 teaspoon of the cold chocolate filling.

  8. Bake the cookies on the center rack, one pan at a time, until firm when pressed near the edge, 8 to 12 minutes. Let stand for 5 minutes, then transfer to wire racks to cool to room temperature.


Make Ahead Tip: Cover and refrigerate the chocolate filling for up to 1 week. Cover and refrigerate the cookie dough for up to 1 day. Store baked cookies airtight in a single layer for up to 3 days or freeze for up to 3 months.

Tip: White whole-wheat flour, made from a special variety of white wheat, is light in color and flavor but has the same nutritional properties as regular whole-wheat flour. It is available at large supermarkets and natural-foods stores and online at or Store it in the freezer.

Nutrition Facts (per serving)

84 Calories
3g Fat
13g Carbs
1g Protein
Nutrition Facts
Servings Per Recipe 48
Serving Size 1 1/2-inch cookie
Calories 84
% Daily Value *
Total Carbohydrate 13g 5%
Dietary Fiber 1g 3%
Total Sugars 7g
Added Sugars 7g 14%
Protein 1g 2%
Total Fat 3g 4%
Saturated Fat 1g 6%
Cholesterol 7mg 2%
Vitamin A 40IU 1%
Vitamin C 0mg 0%
Folate 16mcg 4%
Sodium 30mg 1%
Calcium 18mg 1%
Iron 1mg 4%
Magnesium 5mg 1%
Potassium 27mg 1%

Nutrition information is calculated by a registered dietitian using an ingredient database but should be considered an estimate.

* Daily Values (DVs) are the recommended amounts of nutrients to consume each day. Percent Daily Value (%DV) found on nutrition labels tells you how much a serving of a particular food or recipe contributes to each of those total recommended amounts. Per the Food and Drug Administration (FDA), the daily value is based on a standard 2,000 calorie diet. Depending on your calorie needs or if you have a health condition, you may need more or less of particular nutrients. (For example, it’s recommended that people following a heart-healthy diet eat less sodium on a daily basis compared to those following a standard diet.)

(-) Information is not currently available for this nutrient. If you are following a special diet for medical reasons, be sure to consult with your primary care provider or a registered dietitian to better understand your personal nutrition needs.

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