These cookies are the perfect fall treat! Soft and chewy pumpkin spice cookies serve as the base. The cookie dough is packed with real pumpkin and pumpkin spice, ensuring that every bite has an autumn vibe. Before baking, each cookie is rolled in a pumpkin spice sugar mixture for an extra layer of fall goodness. After baking they get indented in the middle, like a thumbprint pressed down on it. The center is then filled with a simple cream cheese filling. It’s all the flavors of fall in one cookie!

Catch even more fall vibes by making our super moist pumpkin bread or our overnight pumpkin French toast casserole.

Why Our Recipe

  • Thumbprint cookies with a pumpkin spice twist for all the fall vibes.
  • A soft and chewy pumpkin cookie topped with a luscious cream cheese filling.
  • There’s pumpkin and pumpkin spice in the cookie dough, then the cookie is rolled in a pumpkin spice sugar mixture before baking.
An overhead view of pumpkin cheesecake thumbprint cookies on a wire cooling rack.

These melt-in-your-mouth pumpkin cookies are a little piece of heaven and are also surprisingly simple to make. The dough comes together quickly, and the thumbprint technique adds a fun, hands-on step that’s perfect for getting the family involved. Whether you’re baking for a fall get-together, a holiday party, or just because you’re craving something seasonal, these Pumpkin Cheesecake Thumbprint Cookies are sure to be a hit.

Ingredient Notes

An overhead view of the ingredients needed to make pumpkin cheesecake thumbprint cookies.
  • Unsalted Butter: Make sure your butter is softened to room temperature for easy mixing. If you only have salted, reduce the salt in the recipe to 1/4 teaspoon.
  • Pumpkin Purée: Use pure pumpkin purée, not pumpkin pie filling. Pumpkin pie filling contains added sugars and spices, which would alter the recipe.
  • All-Purpose Flour: Stick with regular all-purpose flour here for the right texture.
  • Baking Powder: This helps the cookies rise just slightly, giving them a nice soft texture.
  • Pumpkin Pie Spice: You can use a store-bought blend or make your own with cinnamon, nutmeg, ginger, and cloves.
  • Cream Cheese: Be sure your cream cheese is fully softened before mixing to get a smooth, creamy filling. Cold produces lumps.

Chilling the Dough

Chilling your dough is a crucial step to ensuring the perfect cookie, and you do not want to skip it! Chilling will cool down the butter which will help prevent the cookies from spreading out too fast in the oven. If they spread too fast, there won’t be anything to indent.

A collage of 4 images showing how to indent and fill pumpkin cheesecake thumbprint cookies.

The Perfect Indent

The name “thumbprint cookies” comes from the classic method of using your thumb to press an indentation into the center of the dough. While that works just fine, here are a few other tools and techniques you can use to create a consistent and even shape every time:

Round Teaspoon: This is our preferred method! Use the back of a round teaspoon (1/2 or 1 tablespoon size works well) to gently press down into the warm cookies, making a perfectly round indent.

Knuckle: If you’d like to keep it traditional but want something sturdier than your thumb, try using your knuckle to make the indent. It gives you more control and reduces the risk of cracks.

Wine Cork: For a larger, more uniform indent, a clean wine cork works beautifully. Just press it into the center of the cookies while they’re still warm for a nice, round cavity.

A closeup view of pumpkin cheesecake thumbprint cookies on a wire cooling rack.

Storage Instructions

Refrigerate: Since the cookies contain a cream cheese filling, they should be refrigerated. Store them in an airtight container in the fridge for up to 5 days.

Freeze: For longer storage, freeze the cookies. Place the cooled cookies on a baking sheet and freeze until solid, about 1 hour. Then, transfer them to a resealable freezer bag or airtight container. Freeze for up to 3 months. When ready to serve, thaw the cookies at room temperature.

More pumpkin treats…

Watch the video below where Caytlin will walk you through every step of this recipe. Sometimes it helps to have a visual, and we’ve always got you covered with our cooking show. You can find the complete collection of recipes on YouTube, our Facebook Page, or right here on our website with their corresponding recipes.