Gingerbread Pumpkin Muffin Thumbprints

Featured in: Fresh & Seasonal

Enjoy moist gingerbread muffins infused with pumpkin and a blend of warm spices, baked to a delicate texture and finished with a creamy pumpkin filling pressed into a thumbprint center. Each bite offers harmonious autumn flavors, with subtle notes of ginger, cinnamon, cloves, and nutmeg. Whether served at room temperature or chilled, these treats are ideal for gatherings or cozy moments by yourself. Optional toasted nuts and pairing with spiced chai or cider elevate the experience. Simple prep and bake steps make this a festive addition to any dessert spread.

Updated on Wed, 29 Oct 2025 14:24:00 GMT
Moist gingerbread pumpkin muffin thumbprints topped with creamy filling for autumn delight.  Save
Moist gingerbread pumpkin muffin thumbprints topped with creamy filling for autumn delight. | berrycottage.com

Moist gingerbread muffins infused with pumpkin and warm spices, topped with a creamy pumpkin filling in a thumbprint center—perfect for autumn gatherings and cozy treats.

The first time I made these gingerbread pumpkin muffin thumbprints was for a family fall brunch. Everyone loved the combination of the spicy gingerbread muffin with that creamy pumpkin center—they disappeared quickly!

Ingredients

  • Muffin Base: 1 3/4 cups (220 g) all-purpose flour, 1 teaspoon baking powder, 1/2 teaspoon baking soda, 1/2 teaspoon salt, 2 teaspoons ground ginger, 1 teaspoon ground cinnamon, 1/4 teaspoon ground cloves, 1/4 teaspoon ground nutmeg, 1/2 cup (115 g) unsalted butter (softened), 1/2 cup (100 g) brown sugar, 1/4 cup (60 ml) molasses, 2 large eggs, 3/4 cup (180 ml) pumpkin puree, 1/4 cup (60 ml) milk, 1 teaspoon vanilla extract
  • Pumpkin Cream Filling: 1/2 cup (120 g) cream cheese (softened), 1/4 cup (60 g) pumpkin puree, 1/4 cup (30 g) powdered sugar, 1/2 teaspoon ground cinnamon, 1/2 teaspoon vanilla extract

Instructions

Prep Muffin Tin:
Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease well.
Mix Dry Ingredients:
In a medium bowl, whisk together flour, baking powder, baking soda, salt, ginger, cinnamon, cloves, and nutmeg.
Cream Butter and Sugar:
In a large bowl, cream the butter and brown sugar until light and fluffy. Beat in the molasses and eggs, one at a time.
Add Wet Ingredients:
Mix in pumpkin puree, milk, and vanilla extract until well combined.
Incorporate Dry Ingredients:
Gradually fold in the dry ingredients until just incorporated.
Fill and Bake:
Divide the batter evenly among the muffin cups. Bake for 15 minutes.
Create Thumbprints:
Remove from the oven and carefully press a shallow indent into the center of each muffin.
Complete Baking:
Return muffins to the oven and bake for 5 more minutes or until a toothpick inserted into the muffin (not the center) comes out clean.
Prepare Filling:
Beat together cream cheese, pumpkin puree, powdered sugar, cinnamon, and vanilla until smooth and creamy.
Fill Muffins:
Once muffins are cool, spoon or pipe the pumpkin cream filling into each thumbprint center.
Serve:
Serve at room temperature or chilled.
Warm, spiced gingerbread pumpkin muffin thumbprints with luscious pumpkin cream filling.  Save
Warm, spiced gingerbread pumpkin muffin thumbprints with luscious pumpkin cream filling. | berrycottage.com

My kids always help create the little thumbprints, and watching them stuff the centers with pumpkin cream is a sweet family ritual each November.

Required Tools

You will need a muffin tin, mixing bowls, an electric mixer or whisk, measuring cups and spoons, plus a spoon or piping bag for filling the thumbprints.

Allergen Information

This recipe contains wheat (gluten), dairy (butter, cream cheese, milk), and eggs. If using store-bought ingredients, always check labels for potential allergens.

Nutritional Information

Each muffin contains approximately 240 calories, 10 g total fat, 34 g carbohydrates, and 3 g protein.

Delicious gingerbread pumpkin muffin thumbprints, drizzled with creamy filling for cozy gatherings. Save
Delicious gingerbread pumpkin muffin thumbprints, drizzled with creamy filling for cozy gatherings. | berrycottage.com

Share these spiced treats at your next autumn gathering for a cozy and delicious centerpiece. They're sure to earn compliments from family and friends!

Recipe FAQ

How do I make the thumbprint center in the muffins?

After partially baking, gently press an indent into the center of each muffin with a spoon or your thumb to create space for the filling.

Can I make these muffins gluten-free?

Yes, substitute gluten-free all-purpose flour for regular flour to make a gluten-free batch without sacrificing texture.

What is the best way to store them?

Place the muffins in an airtight container and refrigerate for up to 3 days to maintain freshness and moisture.

Can I use a different filling instead of pumpkin cream?

Feel free to swap the pumpkin cream filling with other creamy fillings like spiced cream cheese, chocolate ganache, or fruit preserves.

Do these muffins pair well with beverages?

They pair wonderfully with hot drinks such as spiced chai, apple cider, or coffee for a cozy experience.

Can I add nuts to the muffin topping?

Yes, sprinkle chopped toasted pecans or walnuts over the filling for extra crunch and flavor.

Gingerbread Pumpkin Muffin Thumbprints

Soft gingerbread muffins filled with pumpkin and warm spices, featuring creamy pumpkin centers—perfect cold weather treat.

Prep duration
20 min
Cook duration
20 min
Complete duration
40 min
Created by Lily Anderson


Complexity Medium

Heritage American

Output 12 Portions

Dietary considerations Meat-free

Components

Muffin Base

01 1 3/4 cups all-purpose flour
02 1 teaspoon baking powder
03 1/2 teaspoon baking soda
04 1/2 teaspoon salt
05 2 teaspoons ground ginger
06 1 teaspoon ground cinnamon
07 1/4 teaspoon ground cloves
08 1/4 teaspoon ground nutmeg
09 1/2 cup unsalted butter, softened
10 1/2 cup brown sugar
11 1/4 cup molasses
12 2 large eggs
13 3/4 cup pumpkin puree
14 1/4 cup milk
15 1 teaspoon vanilla extract

Pumpkin Cream Filling

01 1/2 cup cream cheese, softened
02 1/4 cup pumpkin puree
03 1/4 cup powdered sugar
04 1/2 teaspoon ground cinnamon
05 1/2 teaspoon vanilla extract

Directions

Direction 01

Prepare Oven and Pan: Preheat oven to 350°F. Line a 12-cup muffin tin with paper liners or grease thoroughly.

Direction 02

Mix Dry Ingredients: In a medium bowl, whisk together all-purpose flour, baking powder, baking soda, salt, ground ginger, ground cinnamon, ground cloves, and ground nutmeg.

Direction 03

Cream Butter and Sugar: In a large bowl, beat softened butter and brown sugar together until light and fluffy. Add molasses and eggs, one at a time, mixing after each addition.

Direction 04

Combine Wet Ingredients: Mix in pumpkin puree, milk, and vanilla extract until uniformly blended.

Direction 05

Incorporate Dry Ingredients: Gradually fold the dry ingredient mixture into the wet mixture, stirring just until the batter is combined and no dry streaks remain.

Direction 06

Fill Muffin Tin: Divide the batter evenly between the muffin cups.

Direction 07

Initial Bake and Create Indents: Bake for 15 minutes. Remove from oven and gently press a shallow indent in the center of each muffin using the back of a spoon or your thumb.

Direction 08

Final Bake: Return muffins to oven and bake an additional 5 minutes, until a toothpick inserted into the muffin (avoiding the center) comes out clean.

Direction 09

Make Pumpkin Cream Filling: While muffins cool, beat cream cheese, pumpkin puree, powdered sugar, ground cinnamon, and vanilla extract together until smooth and creamy.

Direction 10

Fill Thumbprints: Pipe or spoon pumpkin cream filling into the indent of each cooled muffin.

Direction 11

Serve: Present at room temperature or chilled as desired.

Necessary tools

  • 12-cup muffin tin
  • Mixing bowls
  • Electric mixer or whisk
  • Measuring cups and spoons
  • Spoon or piping bag

Allergy information

Review each ingredient for potential allergens and seek professional medical advice if you have concerns.
  • Contains wheat (gluten), dairy (butter, cream cheese, milk), and eggs.

Nutritional information (per portion)

These values are estimates only and shouldn't replace professional medical guidance.
  • Energy: 240
  • Fats: 10 g
  • Carbohydrates: 34 g
  • Proteins: 3 g