Quick Gluten-Free Pumpkin Cream Cheese Muffins

Pumpkin Cream Cheese Muffins are the ultimate cozy treat when fall rolls around. These warm, spiced delights combine the earthy sweetness of pumpkin with a creamy, tangy swirl of cream cheese that melts into every bite. They’re naturally gluten-free, yet no one will ever notice — the texture is soft, moist, and bakery-worthy. Whether you’re baking for a brunch crowd, prepping school snacks, or simply craving something sweet with your morning coffee, these muffins deliver all the comfort of pumpkin pie in a grab-and-go package. Bonus: they freeze beautifully and stay delicious for days.

Why You’ll Love This Recipe

this recipe

• Gluten-Free Goodness Without Sacrifice
  Made with a carefully balanced blend of brown rice flour, sorghum flour, and tapioca starch, these muffins are light, fluffy, and full of flavor — no gritty texture or weird aftertaste.
• Cream Cheese Swirl Perfection
  Each muffin hides a sweet and tangy cream cheese center that pairs beautifully with pumpkin spice. It’s like cheesecake and pumpkin bread had a delicious baby.
• Fall Flavors in Every Bite
  Cinnamon, nutmeg, ginger, and cloves bring that unmistakable autumn aroma and taste — perfect for cozy mornings.
• Quick & Simple
  Ready in about 40 minutes from start to finish, this is a stress-free recipe that even beginner bakers can pull off.
• Moist, Tender Texture
  Thanks to pumpkin puree and applesauce, these muffins stay soft for days — no dry crumbs here.

Ingredients

For the Pumpkin Muffin Batter

• ½ cup brown rice flour
• ½ cup sorghum flour
• ½ cup tapioca starch
• 1½ teaspoons ground cinnamon
• 1 teaspoon baking soda
• 1 teaspoon xanthan gum
• ½ teaspoon ground ginger
• ½ teaspoon ground nutmeg
• ½ teaspoon salt
• ⅛ teaspoon ground cloves
• 2 large eggs
• ½ cup packed brown sugar
• ½ cup white sugar
• 1 cup canned pumpkin (100% puree)
• ⅓ cup neutral oil (like avocado or vegetable oil)
• ⅓ cup unsweetened applesauce
• 1 teaspoon vanilla extract

For the Cream Cheese Swirl

• 4 oz cream cheese, softened
• 2 tablespoons white sugar

Optional Toppings

• Chopped pumpkin seeds (pepitas)
• Chopped walnuts or pecans

Instructions

1. Preheat & Prep
   Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners or lightly grease it.
2. Make the Cream Cheese Swirl
   In a small bowl, beat together the softened cream cheese and 2 tablespoons of sugar until smooth. Set aside.
3. Mix the Dry Ingredients
   In a large mixing bowl, whisk together:
   • Brown rice flour
   • Sorghum flour
   • Tapioca starch
   • Cinnamon
   • Baking soda
   • Xanthan gum
   • Ginger
   • Nutmeg
   • Salt
   • Cloves
4. Combine the Wet Ingredients
   In a separate bowl, whisk until smooth:
   • Eggs
   • Brown sugar
   • White sugar
   • Pumpkin puree
   • Oil
   • Applesauce
   • Vanilla extract
5. Mix Wet and Dry
   Pour the wet mixture into the dry ingredients. Stir gently until just combined. Do not overmix — a few streaks of flour are okay.
6. Fill Muffin Cups & Swirl
   Divide the batter evenly between 12 muffin cups. Add about 1 teaspoon of cream cheese mixture on top of each muffin. Use a toothpick to gently swirl the cream cheese into the batter for a marbled look.
7. Add Optional Toppings
   Sprinkle with chopped pepitas, walnuts, or pecans for crunch and color.
8. Bake
   Bake for 20–25 minutes, or until a toothpick inserted in the center comes out clean.
9. Cool & Serve
   Let muffins cool in the pan for 5 minutes before transferring to a wire rack. Serve warm or at room temperature.

Recipe Details & Nutrition Facts

🕒 Recipe Details

• Prep Time: 15–20 minutes
• Cook Time: 20–25 minutes
• Total Time: 35–45 minutes
• Difficulty Level: Medium
• Servings: 12 muffins (approx.)

🥄 Nutrition Facts (Estimated per muffin)

Note: Values are approximate and may vary based on ingredient brands and portion size.

• Calories: 130–150
• Protein: 2–3 g
• Fat: 5–6 g
• Carbohydrates: 20–22 g
• Sugar: 10–12 g
• Fiber: 1–2 g

Tips & Variations

✅ Baking Tips

• Don’t overmix the batter — stir just until no dry streaks remain. Overmixing can make gluten-free muffins dense or gummy.
• Use room-temperature cream cheese for a smoother swirl. Cold cream cheese won’t blend well.
• Let air circulate during storage. Leave one corner of your container cracked open to avoid soggy muffin tops.

🔁 Ingredient Swaps

• Gluten-free flour blend: You can substitute all the flours + xanthan gum with 1½ cups of your favorite 1:1 gluten-free flour mix (with xanthan gum included).
• Pumpkin puree: Try mashed sweet potato or butternut squash for a twist. Mashed banana works too, though it will change the flavor.
• Oil options: Use melted butter, coconut oil, or canola oil. Just make sure melted butter cools slightly before mixing in.
• Spice shortcut: No individual spices? Use 2–3 teaspoons of pumpkin pie spice instead.

🎃 Flavor Variations

• Add chocolate chips or white chocolate chunks for a sweeter treat.
• Mix chopped pecans or dried cranberries into the batter for texture and contrast.
• Sprinkle turbinado sugar on top before baking for a crunchy muffin top.

Pumpkin Cream Cheese Muffins

These gluten-free Pumpkin Cream Cheese Muffins are soft, flavorful, and freezer-friendly. A rich cream cheese swirl takes them from simple to sensational — all in under 45 minutes.

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 25 minutes mins

Total Time 40 minutes mins

Servings: 12 muffins

Course: Dessert

Cuisine: American

Calories: 145

Ingredients Equipment Method Notes

Ingredients

  

• ### For the Muffin Batter:
• – ½ cup brown rice flour
• – ½ cup sorghum flour
• – ½ cup tapioca starch
• – 1½ tsp ground cinnamon
• – 1 tsp baking soda
• – 1 tsp xanthan gum
• – ½ tsp ground ginger
• – ½ tsp ground nutmeg
• – ½ tsp salt
• – ⅛ tsp ground cloves
• – 2 large eggs
• – ½ cup packed brown sugar
• – ½ cup white sugar
• – 1 cup canned pumpkin 100% puree
• – ⅓ cup neutral oil e.g. avocado or vegetable oil
• – ⅓ cup unsweetened applesauce
• – 1 tsp vanilla extract
• ### For the Cream Cheese Swirl:
• – 4 oz cream cheese softened
• – 2 tbsp white sugar
• ### Optional Toppings:
• – Chopped pumpkin seeds walnuts, or pecans

Equipment

• Mixing bowls
• Muffin tin
• Whisk
• – Toothpick or knife (for swirling)
• Measuring cups & spoons

Method

 

1. Preheat oven to **350°F (175°C)**. Line a muffin tin or grease lightly.
2. In a small bowl, mix **cream cheese** and **2 tbsp sugar** until smooth. Set aside.
3. In a large bowl, whisk together all **dry ingredients**.
4. In another bowl, whisk together all **wet ingredients** until smooth.
5. Pour wet mixture into dry, and mix just until combined — do not overmix.
6. Divide batter evenly between 12 muffin cups. Add 1 tsp cream cheese mixture to each muffin and gently swirl with a toothpick.
7. Sprinkle with optional toppings.
8. Bake for **20–25 minutes**, or until a toothpick comes out clean.
9. Cool in pan for 5 mins, then transfer to a wire rack.

Notes

– Don’t overmix the batter to keep muffins light.
– Be sure to use **pure pumpkin puree**, not pie filling.
– Muffins freeze well for up to 3 months.

FAQs

❓ What’s the difference between pumpkin puree and pumpkin pie filling?

Pumpkin puree is just pure cooked pumpkin — no added sugar or spices. Pumpkin pie filling contains sweeteners and seasoning, which can throw off the balance of this recipe. Stick with 100% pure pumpkin.

❓ Can I make these muffins dairy-free?

Yes! Use a dairy-free cream cheese alternative for the swirl (like Kite Hill or Miyoko’s). Make sure it’s plain and unsweetened, and adjust the sugar in the swirl to taste.

❓ Do I have to use all three flours?

For the best texture, yes. But if needed, replace them with 1½ cups of a trusted gluten-free flour blend (that contains xanthan gum) as a shortcut.

❓ Can I freeze these muffins?

Absolutely! Wrap them individually and freeze for up to 3 months. To reheat, thaw at room temp or microwave for 20–30 seconds.

❓ How do I store leftovers?

Store in an airtight container at room temp for up to 2 days, then move to the fridge for up to a week. For best results, allow a bit of airflow to prevent sogginess.

Conclusion

These Pumpkin Cream Cheese Muffins are everything you love about fall — warm spices, creamy swirls, and cozy vibes — all wrapped in a gluten-free package that no one will guess is allergy-friendly. Whether you’re baking for guests or just treating yourself, this easy recipe delivers big flavor with minimal fuss. Keep a batch on hand for chilly mornings or those mid-afternoon pumpkin cravings. They’re the kind of muffins you’ll look forward to all season long.