Soft Pumpkin Thumbprint Cookies With Apple Butter or Nutella

These pumpkin thumbprint cookies are soft, lightly spiced cookies with a cake-like texture and a sweet filled center. They aren’t the traditional crumbly shortbread-style thumbprint cookie. Pumpkin puree and baking powder give these cookies a slight rise and a softer bite.

I tested the cookies with both apple butter and Nutella, and both work nicely with the cinnamon, ginger and nutmeg in the pumpkin cookie. There is one important difference in how these are made: don’t press the thumbprint into the dough before baking. The cookies rise enough that the indentation will disappear. Instead, bake them first and press the divot into each cookie as soon as it comes out of the oven.

Quick Answer

These pumpkin thumbprint cookies are soft, lightly spiced pumpkin cookies with a tender, cake-like texture and apple butter or Nutella centers. Chill the dough for at least 30 minutes, bake until light orange-gold and dry on the surface, then press the thumbprint into each warm cookie after baking so the slight rise doesn’t make the indentation disappear.

For a more traditional buttery thumbprint cookie, my Mincemeat Butter Thumbprint Cookies use a firmer cookie base.

I wanted to create a soft, lightly spiced fall cookie that was versatile enough to handle different fillings without the pumpkin spice overwhelming everything else. Apple butter adds another layer of warm spice and fruit, giving the pumpkin cookie base a much stronger punch of fall flavour. Filling the same lightly flavoured pumpkin cookie with Nutella takes it in a completely different direction—the chocolate-hazelnut center is sweeter and more familiar, which makes that version especially nice for kids at fall gatherings. Making both from one batch also gives you an easy way to offer two very different cookies without making two separate doughs.

Why You’ll Love These Pumpkin Thumbprint Cookies

Soft, Cakey Pumpkin Texture: These aren’t traditional shortbread thumbprint cookies. Pumpkin puree and baking powder give them a soft, tender, cake-like texture with just enough structure to hold the filled center.

Two Fall-Friendly Filling Options: Fill them with homemade apple butter for an extra layer of warm spice and fruit flavor, or use Nutella for a sweeter chocolate-hazelnut version that is especially kid-friendly for fall gatherings.

Easy To Customize From One Batch: The lightly spiced pumpkin cookie base works with different fillings, so you can make a mixed batch without preparing two separate cookie doughs.

How To Make Pumpkin Thumbprint Cookies

Start by combining the butter, sugar and pumpkin puree until the mixture is evenly blended. Add the cinnamon, ginger and nutmeg, mixing until the spices are distributed throughout the pumpkin mixture.

Add the flour and baking powder and mix just until a soft pumpkin cookie dough forms.

Cover the dough and refrigerate it for at least 30 minutes. The chilled dough will be firmer and easier to roll into balls. While the dough chills, line a cookie sheet with parchment paper and preheat the oven to 375°F.

Roll the chilled dough into balls and arrange them on the prepared cookie sheet, leaving a little room between each cookie. Do not make the thumbprint indentation before baking. These pumpkin cookies rise slightly in the oven, and an indentation made in the raw dough can disappear as the cookie puffs.

Bake the pumpkin thumbprint cookies for 8–10 minutes. Watch the cookies rather than relying only on the timer. They are ready when they have a light orange-gold colour and the surface looks visibly dry rather than wet or shiny. The cookies should still be soft rather than browned or crisp.

As soon as the cookies come out of the oven, use the back of a small spoon to gently press a divot into the center of each warm cookie. The soft cookie will hold the indentation, or cookie well, as it cools.

Once the centers are formed, fill each cookie with apple butter or Nutella. The apple butter gives the lightly spiced pumpkin cookie a stronger fall flavour, while the chocolate-hazelnut filling gives you a sweeter, milder version.

Ingredients For Pumpkin Thumbprint Cookies

These pumpkin thumbprint cookies use a simple pumpkin cookie dough flavoured with cinnamon, ginger and nutmeg, with apple butter or Nutella added to the centers after baking.

Butter: Adds richness and tenderness to the soft pumpkin cookie dough. Chilling the finished dough firms the butter again so the cookies are easier to roll before baking.

Pumpkin Puree: Adds pumpkin flavour, moisture and the natural orange-gold colour. Use plain pumpkin puree rather than prepared pumpkin pie filling.

White Sugar: Sweetens the cookie while keeping the flavour light enough for either apple butter or Nutella to work as the filling.

Cinnamon: Provides the strongest warm-spice note in the cookie without overpowering the pumpkin.

Ginger: Adds a little warmth and helps build the fall spice flavour.

Nutmeg: Rounds out the cinnamon and ginger with a warmer background spice.

All-Purpose Flour: Gives the pumpkin cookie dough enough structure to be rolled into balls after chilling while still producing a soft, cake-like cookie.

Baking Powder: Gives these cookies their slight rise and soft texture. That rise is also why the thumbprint is pressed into the cookies after baking rather than before.

Apple Butter: Adds concentrated apple flavour and another layer of warm spice. My homemade apple butter works especially well with the lightly spiced pumpkin base.

Nutella or Chocolate-Hazelnut Spread: Gives the same pumpkin cookie a sweeter chocolate-hazelnut center and makes a milder option for kids and fall gatherings.

Substitutions And Add-Ins For Pumpkin Thumbprint Cookies

Pumpkin Pie Spice: You can replace the cinnamon, ginger and nutmeg with about 1¾ teaspoons of my homemade pumpkin spice blend if that is what you keep on hand. The original recipe was tested with the individual spices, which gives better control over the lightly spiced flavour.

Apple Butter: Use homemade apple butter or your favourite prepared apple butter. This is the filling to choose when you want the strongest fall flavour because the spiced apple layer builds on the pumpkin and warm spices in the cookie.

Nutella or Chocolate-Hazelnut Spread: Nutella can be replaced with another thick chocolate-hazelnut spread. This gives the cookie a sweeter, more chocolate-forward center while leaving the lightly spiced pumpkin base noticeable.

Use Two Fillings In One Batch: There is no need to choose just one. Fill half of the cookies with apple butter and the other half with chocolate-hazelnut spread for an easy mixed cookie tray.

Other Thick Fillings: A thick fruit butter or spread may work in the baked divot, but I have only tested these cookies with apple butter and Nutella. Avoid thin or runny fillings, which are more likely to spill over the shallow center.

Adding Nuts: If you want extra texture, finely chopped pecans or walnuts could be sprinkled over the filled centers rather than mixed into the dough. This keeps the texture and structure of the tested pumpkin cookie base intact.

Expert Tips, Serving And Storing Suggestions For Pumpkin Thumbprint Cookies

Tip #1: Chill The Dough For At Least 30 Minutes: Pumpkin puree adds moisture to the cookie dough, so chilling firms the dough enough to roll and helps the cookies hold their shape as they bake.

Tip #2: Don’t Make The Divot Before Baking. These pumpkin cookies have a slight rise from the baking powder. If you press the thumbprint into the raw dough, it can puff back up and disappear in the oven.

Tip #3: Press The Centers While The Cookies Are Warm. As soon as the cookies come out of the oven, gently press the back of a small spoon into the center of each one. The warm, soft cookie is easy to shape and will hold the divot as it cools.

Tip #4: Watch The Surface For Doneness. The cookies are ready when they are a light orange-gold colour and the surface looks dry rather than wet or shiny. They should still be soft and do not need to become deeply browned.

Serving Suggestions

These soft pumpkin thumbprint cookies are a nice addition to a fall cookie platter or Thanksgiving dessert table. For a mixed autumn baking tray, serve them alongside my Apple Crisp Cookies or Soft Baked Pumpkin Donuts for a combination of apple and pumpkin desserts.

The apple butter-filled cookies pair especially well with coffee or tea, while the Nutella version is a fun choice for kids at fall gatherings. If you are planning a larger pumpkin baking spread, my Pumpkin Spice Scones give you another way to use those warm cinnamon, ginger and nutmeg flavours.

Storing Pumpkin Thumbprint Cookies

Allow the cookies to cool completely before placing them in an airtight container. Because these are soft, cake-like pumpkin cookies, keeping them well covered helps prevent the surface and edges from drying out.

If you are using apple butter, store the filled cookies according to the storage requirements of the apple butter you use. My small-batch stovetop apple butter is refrigerated after opening, so cookies filled with it should also be kept refrigerated.

For the best texture, you can also store the baked cookies unfilled and add the apple butter or Nutella shortly before serving. This keeps the soft pumpkin cookie from sitting against the filling for an extended period.

These soft pumpkin thumbprint cookies are a fun change from traditional shortbread thumbprints, especially when you want a fall cookie with a softer, cake-like texture. Apple butter gives them a stronger warm-spiced fall flavour, while Nutella makes the same lightly spiced pumpkin cookie sweeter and more familiar for kids.

The most important thing to remember is to make the thumbprint after baking. Pressing the cookie well while the cookies are still warm gives you a defined center without losing it to the slight rise in the oven.

If you make both fillings, let me know which your family prefers—the spiced apple butter or the chocolate-hazelnut center.

Meet Amber

I’m the home cook and recipe creator behind A Cents For Cookery. I learned to cook growing up off-grid in Northern Ontario, where meals were made on a woodstove and preserving, baking, and making ingredients stretch were part of everyday life. Here I share practical family recipes, homemade baking, vintage-inspired cooking, and the kitchen knowledge I’ve picked up over the years to help you make the most of the food you have.

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