Quick Gluten-Free Pumpkin Cream Cheese Muffins

Pumpkin Cream Cheese Muffins are the perfect way to welcome fall—warm, spiced, and irresistibly soft with a creamy surprise in every bite. Whether you’re hosting brunch, packing lunchboxes, or simply craving something cozy, these muffins offer all the autumn vibes without the gluten. As a chef who’s baked through countless fall seasons, I can confidently say this recipe balances flavor and texture so well, no one will guess they’re gluten-free. With a luscious cream cheese swirl and that golden pumpkin color, they look bakery-worthy but come together with simple ingredients you already have at home.

💛 Why You’ll Love This Recipe

• Gluten-free, without compromise – These Pumpkin Cream Cheese Muffins are soft, moist, and bakery-worthy, thanks to a smart mix of gluten-free flours that won’t leave you missing the wheat.
• Creamy center in every bite – The sweetened cream cheese swirl melts right into the muffin, giving you a tangy contrast to the warm pumpkin spices.
• Fast & fuss-free – From mixing bowl to oven in under 20 minutes, they’re simple enough for weekday mornings but elegant enough for weekend guests.
• Fall flavor perfection – A balanced blend of cinnamon, nutmeg, ginger, and cloves gives that unmistakable pumpkin spice aroma we all crave.
• Great for prepping ahead – These muffins freeze beautifully and stay moist for days, making them ideal for busy mornings or snack breaks.

🧾 Ingredients for Pumpkin Cream Cheese Muffins

Here’s everything you need to make these soft, flavorful Pumpkin Cream Cheese Muffins from scratch:

🧁 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% pure pumpkin)
• ⅓ cup neutral oil (like canola or vegetable)
• ⅓ cup unsweetened applesauce
• 1 tsp vanilla extract

🍥 Cream Cheese Swirl

• 4 oz cream cheese, softened to room temp
• 2 tbsp white sugar

🥄 Optional Toppings

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

👩‍🍳 Instructions

Follow these step-by-step directions to make perfectly tender and creamy Pumpkin Cream Cheese Muffins every time:

1. Prepare the Cream Cheese Swirl

• In a small bowl, combine 4 oz cream cheese and 2 tbsp sugar.
• Mix until smooth and creamy. Set aside.

2. Mix the Dry Ingredients

• In a large bowl, whisk together:
  • ½ cup brown rice flour
  • ½ cup sorghum flour
  • ½ cup tapioca starch
  • 1½ tsp cinnamon
  • 1 tsp baking soda
  • 1 tsp xanthan gum
  • ½ tsp ginger
  • ½ tsp nutmeg
  • ½ tsp salt
  • ⅛ tsp cloves

3. Mix the Wet Ingredients

• In another bowl, whisk together:
  • 2 large eggs
  • ½ cup packed brown sugar
  • ½ cup white sugar
  • 1 cup canned pumpkin
  • ⅓ cup neutral oil
  • ⅓ cup unsweetened applesauce
  • 1 tsp vanilla extract

4. Combine Wet and Dry

• Pour the wet mixture into the bowl with the dry ingredients.
• Gently fold together until just combined — do not overmix, or your muffins may become dense.

5. Assemble the Muffins

• Preheat your oven to 350°F (175°C).
• Line or grease a muffin tin.
• Fill each muffin cup about ¾ full with batter.
• Drop a heaping teaspoon of the cream cheese mixture into the center of each muffin.
• Use a toothpick or knife to gently swirl it in. Don’t overdo it—just a few turns.

6. Add Optional Toppings

• Sprinkle with pumpkin seeds, walnuts, or pecans for extra crunch and visual appeal.

7. Bake and Cool

• Bake for 20–25 minutes, or until a toothpick inserted near the center comes out clean (a little cream cheese is fine).
• Cool in the pan for 5 minutes, then transfer to a wire rack to finish cooling.

⏱️ Recipe Details

• Prep Time: 15–20 minutes
• Cook Time: 20–25 minutes
• Total Time: 35–45 minutes
• Difficulty: Medium
• Servings: Makes about 12 muffins

🧮 Nutrition Facts (Per Muffin – Estimated)

While exact numbers vary based on toppings and cream cheese amounts, here’s an estimate per muffin (assuming 12 muffins total):

• Calories: ~130–145
• Protein: ~2 g
• Fat: ~5–6 g
• Carbohydrates: ~20–22 g
• Sugar: ~10–12 g
• Fiber: ~1 g

💡 Note: These numbers are approximations and should not be used for medical dietary planning.

🔄 Tips & Variations

✅ Pro Tips for Perfect Muffins

• Don’t overmix the batter — gluten-free flours can become gummy if stirred too much. Mix until ingredients are just combined.
• Room temperature cream cheese is key for a smooth swirl. Cold cream cheese won’t blend as easily into the muffin batter.
• Use pure pumpkin puree, not pumpkin pie filling. The added sugars and spices in pie filling can throw off the recipe.
• To avoid soggy muffins, store with the lid slightly ajar or use a paper towel in the container to absorb extra moisture.

🧁 Easy Variations

• Make it dairy-free: Use dairy-free cream cheese or thick coconut yogurt with powdered sugar for the swirl.
• Use a spice blend: No ground cloves or ginger? Swap them all for 2–3 tsp of pumpkin pie spice.
• Nut-free version: Skip the topping or use sunflower seeds instead of nuts.
• Add-ins: Mini chocolate chips, dried cranberries, or chopped dates make a fun twist for extra flavor or texture.

❓ FAQs

Can I use a gluten-free flour blend instead of individual flours?

Absolutely! Swap the brown rice, sorghum, and tapioca starch for 1½ cups of a gluten-free flour blend that contains xanthan gum. If your mix already has xanthan gum, leave it out of the recipe.

How do I store these Pumpkin Cream Cheese Muffins?

Store in an airtight container at room temperature for up to 2 days. After that, refrigerate to keep them fresh for up to a week. For best results, allow them to come to room temp before serving.

Can I freeze these muffins?

Yes! Wrap each muffin individually or store them in a freezer-safe container. Freeze for up to 3 months. To serve, thaw at room temperature for 30 minutes or microwave for 20–30 seconds.

What can I use instead of cream cheese?

Try mascarpone or thick Greek yogurt mixed with a little powdered sugar. These won’t be as rich, but they’ll still offer a nice creamy contrast.

What should I serve with these muffins?

They pair wonderfully with a hot cup of coffee, chai tea, or apple cider. For a fall brunch, serve with scrambled eggs, bacon, or a side of Greek yogurt with honey.

🎉 Conclusion

These Pumpkin Cream Cheese Muffins bring together everything we love about fall baking—warm spices, creamy centers, and tender, fluffy texture—all without a trace of gluten. Whether you’re making a batch for brunch, freezing them for busy mornings, or sharing them with friends, this recipe is sure to become a seasonal staple in your kitchen. Once you taste that cozy combo of pumpkin spice and sweet cream cheese, you’ll be making these on repeat.