Pumpkin Cream Cheese Muffins: The Coziest Fall Baking Treat

There’s something magical about autumn—the crisp air, colorful leaves crunching underfoot, and of course, the irresistible call of fall baking. And nothing captures that cozy, sweater-weather vibe quite like Pumpkin Cream Cheese Muffins. They’re everything you love about pumpkin muffins, but with a sweet surprise tucked inside: a rich cream cheese filling that makes every bite feel extra indulgent.

These little beauties are the kind of spiced muffins that fill your kitchen with aromas so heavenly, even your neighbors might “accidentally” stop by. They’re soft, moist, perfectly sweetened with maple syrup or honey, and topped with a candied ginger crunch that feels just fancy enough to impress but simple enough for a weekday treat.

Whether you’re baking for a family brunch, packing lunchbox surprises, or simply craving a cozy dessert with your afternoon coffee, these muffins will become your go-to recipe.

Why You’ll Love These Pumpkin Cream Cheese Muffins

• Perfect balance of flavors – Sweet pumpkin meets tangy cream cheese.

• Fall vibes in every bite – Cinnamon, ginger, nutmeg, and cloves bring warm spice.

• Moist and tender – Pumpkin puree keeps these muffins soft.

• Easy enough for beginners – A no-fuss recipe with bakery-style results.

• Cozy desserts for all occasions – Breakfast, snack, or after-dinner sweet.

Ingredients

Muffin Batter

• ½ cup melted coconut oil (120 ml)

• ½ cup + 1 tbsp maple syrup or honey (125 ml + 15 ml)

• 1 tbsp vanilla extract (15 ml)

• 2 large eggs, room temperature

• ¾ cup pumpkin butter (180 g)

• ¾ cup pumpkin puree (180 g)

• 1 ½ cups white whole wheat flour (180 g)

• 1 ½ tsp baking powder (6 g)

• ½ tsp baking soda (3 g)

• 1 tsp ground cinnamon (3 g)

• ½ tsp ground ginger (1.5 g)

• ⅛ tsp cardamom (0.3 g)

• ⅛ tsp nutmeg (0.3 g)

• ⅛ tsp ground cloves (0.3 g)

• 1 tsp kosher salt (6 g)

• 2 tbsp candied ginger pieces (20 g)

Cream Cheese Filling

• 8 oz cream cheese, softened (225 g)

• 1 tbsp maple syrup or honey (15 ml)

Sugared Ginger Topping

• ¼ cup candied ginger pieces (60 g)

• 1 tbsp cinnamon sugar (12 g)

Step-by-Step Directions

1. Preheat oven. Heat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.

2. Mix wet ingredients. In a large bowl, whisk coconut oil, ½ cup maple syrup or honey, vanilla, eggs, pumpkin butter, and pumpkin puree until smooth.

3. Add dry ingredients. Stir in flour, baking powder, baking soda, spices, and salt. Mix gently—don’t overwork the batter. Fold in candied ginger. Divide batter evenly into muffin cups (about ¾ full).

4. Make the filling. In a small bowl, beat cream cheese with 1 tbsp maple syrup or honey until fluffy. Drop 1 rounded teaspoon into each muffin center, pressing slightly so it sinks halfway.

5. Top it off. Sprinkle the candied ginger–cinnamon sugar topping over each muffin.

6. Bake. Place in oven for 18–20 minutes, until golden and set. Cool for 5 minutes before removing from the pan. Best enjoyed warm.

Baking Tips for Pumpkin Cream Cheese Muffins

• Don’t overmix. Stir the batter just until combined. Overmixing = tough muffins.

• Room temp cream cheese. Softened cream cheese blends smoother for a creamy center.

• Make them ahead. Bake a batch and freeze for quick fall treats.

• Switch up the spices. If you don’t have cardamom, just add a touch more cinnamon or nutmeg.

• Topping tip. For extra crunch, add chopped pecans or walnuts along with the candied ginger.

My Pumpkin Muffin Story

These muffins became my “welcome to fall” tradition a few years back. Every September, when the first cool breeze rolled in, I’d head to the kitchen and whip up a batch. I remember my daughter walking in from school one afternoon, dropping her backpack, and saying, “Mom, it smells like fall in here!” That was it—the official start of pumpkin season.

Now, it’s become a family ritual. The kids sneak spoonfuls of the cream cheese filling while I’m not looking, my husband hovers near the oven like a watchdog, and before I know it, half the batch disappears within minutes of cooling. These muffins aren’t just a recipe—they’re little markers of autumn memories.

What to Serve with Pumpkin Cream Cheese Muffins

These muffins are lovely on their own, but pairing them with the right side makes them even more special:

• Morning coffee or chai latte – The warm spices pair perfectly with cozy drinks.

• Fresh fruit – A simple side of apple slices or pears balances the richness.

• After-dinner treat – Serve slightly warmed with a dollop of whipped cream for dessert.

• Holiday brunch – Add them to your fall or Thanksgiving spread.

How to Store Pumpkin Cream Cheese Muffins

• Room temperature: Keep in an airtight container for up to 2 days.

• Refrigerator: Because of the cream cheese filling, they’ll last up to 5 days chilled.

• Freezer-friendly: Wrap individually in plastic and freeze for up to 2 months. Thaw overnight or microwave for 30 seconds.

• Pro tip: Warm them slightly before eating to bring back that fresh-baked magic.

FAQs About Pumpkin Cream Cheese Muffins

Can I make these without pumpkin butter?

Yes! Double the pumpkin puree and add an extra teaspoon of cinnamon for flavor.

Can I use store-bought pumpkin muffins and add filling?

You could, but honestly, these are so easy you won’t need the shortcut.

Can I make mini muffins?

Absolutely—just reduce bake time to about 12–14 minutes.

Do I have to use candied ginger?

Not at all. Try chopped nuts, chocolate chips, or leave the topping off.

Can these be made gluten-free?

Yes—substitute a good gluten-free flour blend for the wheat flour.

Wrapping Up with Fall Flavor

If autumn had a flavor, it would be these Pumpkin Cream Cheese Muffins. Warm, spiced, creamy, and just sweet enough—they’re the muffins you’ll bake again and again all season long. Whether you’re making them for breakfast, dessert, or just because, they’ll fill your kitchen (and your heart) with cozy vibes.

So grab your mixing bowl, pull on your favorite sweater, and let these muffins bring a little extra joy to your fall baking adventures.

Discover more delicious recipes by following me on Facebook and Pinterest.

Pumpkin Cream Cheese Muffins

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• Author: Olivia Hartwellen
• Total Time: 40 minutes
• Yield: 12 muffins 1x
• Diet: Vegetarian

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Description

Pumpkin Cream Cheese Muffins are the ultimate cozy fall baking treat—soft, spiced pumpkin muffins with a creamy, sweet cream cheese center and a candied ginger crunch on top. Perfectly balanced between warm autumn spices and tangy filling, these muffins are easy to make yet feel bakery-worthy. Ideal for breakfast, snacks, or holiday brunch spreads, they’re a fall tradition in every bite.

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Ingredients

Scale 1x2x3x

Muffin Batter

• ½ cup (120 ml) melted coconut oil

• ½ cup + 1 tbsp (140 ml) maple syrup or honey

• 1 tbsp (15 ml) vanilla extract

• 2 large eggs, room temperature

• ¾ cup (180 g) pumpkin butter

• ¾ cup (180 g) pumpkin puree

• 1 ½ cups (180 g) white whole wheat flour

• 1 ½ tsp (6 g) baking powder

• ½ tsp (3 g) baking soda

• 1 tsp (3 g) ground cinnamon

• ½ tsp (1.5 g) ground ginger

• ⅛ tsp (0.3 g) cardamom

• ⅛ tsp (0.3 g) nutmeg

• ⅛ tsp (0.3 g) ground cloves

• 1 tsp (6 g) kosher salt

• 2 tbsp (20 g) candied ginger pieces

Cream Cheese Filling

• 8 oz (225 g) cream cheese, softened

• 1 tbsp (15 ml) maple syrup or honey

Sugared Ginger Topping

• ¼ cup (60 g) candied ginger pieces

• 1 tbsp (12 g) cinnamon sugar

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Instructions

• Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.

• In a large bowl, whisk together coconut oil, ½ cup maple syrup/honey, vanilla, eggs, pumpkin butter, and pumpkin puree until smooth.

• Add flour, baking powder, baking soda, spices, and salt. Stir gently until just combined. Fold in candied ginger. Divide batter into muffin cups (¾ full).

• In a small bowl, beat cream cheese with 1 tbsp maple syrup/honey until fluffy. Drop 1 rounded teaspoon into the center of each muffin. Press slightly so it sinks halfway.

• Mix candied ginger with cinnamon sugar. Sprinkle topping over muffins.

• Bake 18–20 minutes, until golden and set. Cool 5 minutes before removing from pan. Enjoy warm.

Notes

Don’t overmix batter—this keeps muffins tender.

Use room temperature cream cheese for a smooth filling.

Can be frozen up to 2 months (wrap individually).

Substitute candied ginger with chopped nuts or chocolate chips.

To make gluten-free, use a 1:1 GF flour blend.

• Prep Time: 20 minutes
• Cook Time: 20 minutes
• Category: Desserts / Baked Goods
• Method: Baking
• Cuisine: American