Pumpkin cream cheese muffins are the ultimate fall treat—moist, warmly spiced, and filled with a creamy surprise in every bite. Whether you’re gluten-free or just love a good seasonal bake, these muffins strike the perfect balance between cozy comfort and bakery-level indulgence. Each one features a tender pumpkin base swirled with sweetened cream cheese and topped with a little crunch for good measure. The best part? They come together in under 45 minutes, making them perfect for busy mornings or spontaneous weekend baking. If you’ve been craving a muffin that tastes like fall in a wrapper, this recipe is your new go-to.
❤️ Why You’ll Love This Recipe
These pumpkin cream cheese muffins check all the boxes for a crowd-pleasing, seasonal bake—without the gluten. Here’s why they’ll become a staple in your kitchen this fall:
- Gluten-Free, No Compromises
Made with a carefully balanced blend of brown rice flour, sorghum flour, and tapioca starch, these muffins are tender, not gritty or dry. - Cream Cheese Surprise in Every Bite
A luscious, tangy cream cheese swirl runs through the center, adding creamy richness to every mouthful. - Full of Cozy Fall Flavor
Warm spices like cinnamon, nutmeg, ginger, and cloves create that nostalgic autumn aroma that fills your whole kitchen. - Quick and Convenient
From prep to plate in under 45 minutes—perfect for weekday breakfasts or relaxed weekend brunches. - Moist and Tender Texture
Thanks to pumpkin puree and applesauce, each bite stays soft and flavorful for days.
📝 Ingredients
Here’s everything you’ll need to make these irresistibly soft and flavorful pumpkin cream cheese muffins. This recipe includes three parts: the muffin batter, the cream cheese swirl, and optional toppings for added texture and flavor.
For the Pumpkin 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 (pure pumpkin puree)
- ⅓ cup neutral oil (e.g., vegetable or avocado 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 (pepitas)
- Chopped walnuts or pecans
These ingredients come together for that perfect moist texture with a tangy swirl and a little crunch on top. Don’t worry if you’re missing a spice or two—you’ll find substitutions and variations later in the post.
👩🍳 Instructions
Follow these simple steps to make bakery-style pumpkin cream cheese muffins right at home. Be sure not to overmix the batter to keep your muffins light and tender!
1. Make the Cream Cheese Swirl
- In a small bowl, combine 4 oz cream cheese and 2 tbsp white sugar.
- Mix until smooth and creamy. Set aside.
2. Mix the Dry Ingredients
- In a large mixing bowl, whisk together:
- 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
3. Mix the Wet Ingredients
- In another bowl, whisk until combined:
- 2 large eggs
- ½ cup packed brown sugar
- ½ cup white sugar
- 1 cup pumpkin puree
- ⅓ cup neutral oil
- ⅓ cup unsweetened applesauce
- 1 tsp vanilla extract
4. Combine Wet and Dry Ingredients
- Pour the wet ingredients into the dry.
- Gently fold the mixture together until just combined—do not overmix!
5. Assemble the Muffins
- Preheat your oven to 350°F (175°C) and line or grease a muffin tin.
- Fill each muffin cup about ¾ full with batter.
- Spoon about 1 tsp of the cream cheese mixture on top of each.
- Use a toothpick or knife to swirl the cream cheese slightly into the batter.
- Optional: Sprinkle with pumpkin seeds, walnuts, or pecans.
6. Bake and Cool
- Bake for 20–25 minutes, or until a toothpick comes out clean.
- Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
⏱️ Recipe Details & Nutrition
Here’s everything you need to know to prep, bake, and plan for these delightful pumpkin cream cheese muffins—plus a look at their nutritional profile.
📋 Recipe Details
- Prep Time: 15–20 minutes
- Cook Time: 20–25 minutes
- Total Time: 35–45 minutes
- Difficulty Level: Medium
- Servings: Makes about 12 standard muffins
🔢 Estimated Nutrition Facts (per muffin, approximate)
Based on a batch of 12 muffins and excluding optional toppings:
- Calories: 130–150
- Protein: 2–2.5 g
- Fat: 5–6 g
- Carbohydrates: 20–22 g
- Sugar: 10–12 g
- Fiber: ~1 g
These muffins are a great way to satisfy a sweet craving without overindulging, and they freeze beautifully for meal prep or lunchbox treats!
🧁 Tips & Variations
Want to make sure your pumpkin cream cheese muffins come out perfect every time? These expert tips and creative variations will help you bake with confidence—and maybe even switch things up!
✅ Pro Tips for Success
- Don’t Overmix the Batter
Mix just until the dry ingredients disappear. Overmixing will make the muffins dense and gummy—especially in gluten-free baking. - Use Room Temperature Cream Cheese
Cold cream cheese won’t swirl properly. Let it sit out or microwave for 10 seconds if needed. - Watch the Bake Time
Every oven is different. Start checking at 20 minutes. A toothpick inserted into the muffin (not the cream cheese) should come out clean. - Let Air Circulate When Storing
To prevent stickiness, crack the container lid slightly if storing at room temp.
🔄 Easy Variations
- Dairy-Free?
Use a plant-based cream cheese (like Kite Hill or Tofutti) and a neutral oil like avocado or coconut oil. - Add a Crunchy Topping
Mix pumpkin seeds with a pinch of cinnamon sugar before sprinkling over the batter for a bakery-style finish. - Spice Swap
No cinnamon, ginger, nutmeg, or cloves? Sub in 2–3 tsp of pumpkin pie spice instead. - Flavor Twists
Try adding:- ¼ cup mini chocolate chips
- A handful of chopped dried cranberries
- A sprinkle of orange zest to the batter for brightness
Pumpkin Cream Cheese Muffins
Ingredients
Equipment
Method
- Prepare the Cream Cheese Swirl:
- In a small bowl, mix softened cream cheese and sugar until smooth. Set aside.
- Mix Dry Ingredients:
- In a large bowl, whisk together brown rice flour, sorghum flour, tapioca starch, cinnamon, baking soda, xanthan gum, ginger, nutmeg, salt, and cloves.
- Mix Wet Ingredients:
- In another bowl, whisk eggs, brown sugar, white sugar, pumpkin puree, oil, applesauce, and vanilla extract until combined.
- Combine Wet & Dry Mixtures:
- Pour the wet ingredients into the dry mixture and fold gently until just combined. Do not overmix.
- Assemble the Muffins:
- Preheat oven to 350°F (175°C) and line or grease a muffin tin.
- Fill each cup ¾ full with batter. Add 1 tsp cream cheese mixture on top and gently swirl with a toothpick.
- Optionally, sprinkle pumpkin seeds or chopped nuts on top.
- Bake:
- Bake for 20–25 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese) comes out clean.
- Cool & Serve:
- Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Notes
❓FAQs
Can I use a store-bought gluten-free flour blend?
Absolutely! If you don’t want to mix your own flours, replace the brown rice, sorghum, and tapioca with 1½ cups of a gluten-free blend that contains xanthan gum. If your blend already includes it, skip the added xanthan gum in the recipe.
Is it okay to use pumpkin pie filling instead of puree?
Nope—stick to 100% pumpkin puree. Pumpkin pie filling is pre-sweetened and spiced, which will throw off the balance of flavors and sweetness in the muffins.
What can I substitute for applesauce?
You can replace applesauce with:
- Extra oil (use ⅔ cup oil total)
- Greek yogurt
- Mashed ripe banana
Each option slightly changes the flavor and texture.
How do I store these muffins?
- Room Temp: Airtight container for up to 1 day
- Refrigerated: Up to 5–6 days
- Freezer: Wrap individually and freeze up to 3 months
How do I thaw frozen muffins?
Let them thaw at room temperature for 30 minutes or microwave on medium for 20–30 seconds. They’ll taste fresh and creamy again in no time!
🍂 Conclusion
These pumpkin cream cheese muffins are everything you want in a fall bake—warm, spiced, creamy, and completely gluten-free. Whether you’re baking for a cozy morning at home or packing snacks for the week, this recipe delivers rich pumpkin flavor and a delightful cream cheese swirl in every bite. They freeze beautifully, adapt well to substitutions, and are easy enough for beginner bakers. Keep a batch on hand and watch them disappear fast!