These Pumpkin Cheesecake Muffins are a delicious blend of cozy fall spices and creamy cheese filling. They’re perfect for breakfast or a sweet snack!
Each bite is like a mini celebration of pumpkin goodness, with a delightful surprise of cream cheese in the center. I love having these with my morning coffee. You will too!
Key Ingredients & Substitutions
All-Purpose Flour: This forms the base of your muffins. If you’re looking for a gluten-free option, use a gluten-free flour blend. Just ensure it contains a binding agent like xanthan gum!
Pumpkin Puree: Use canned pumpkin for convenience. If you have fresh pumpkin, you can roast it, then puree it. Just be sure to drain it well to avoid excess moisture!
Pumpkin Pie Spice: If you don’t have this on hand, mix 1 tsp cinnamon, 1/2 tsp nutmeg, and 1/4 tsp each of ginger and cloves together. Spice it up to your taste!
Cream Cheese: Use full-fat cream cheese for the best creamy filling. If you need a lighter option, you can use reduced-fat cream cheese or even Greek yogurt for a creamy twist.
What’s the Best Way to Combine Ingredients Without Overmixing?
The key to tender muffins is not to overmix the batter once you combine the wet and dry ingredients. Overmixing can lead to dense muffins.
- First, gently pour the wet ingredients into the bowl of dry ingredients.
- Use a spatula or wooden spoon to fold them together just until you don’t see any dry flour. This might leave some lumps, and that’s perfectly okay!
- Stop mixing as soon as everything is combined, and you’re good to go. This keeps the muffins light and fluffy.
Remember, it’s normal for the batter to look imperfect. Happy baking!

Pumpkin Cheesecake Muffins With Cream Cheese Filling
Ingredients You’ll Need:
For the Muffins:
- 1 3/4 cups (220g) all-purpose flour
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp salt
- 2 tsp pumpkin pie spice (or a blend of cinnamon, ginger, nutmeg, and cloves)
- 3/4 cup (150g) granulated sugar
- 1/2 cup (100g) brown sugar, packed
- 1 cup (240ml) canned pumpkin puree
- 2 large eggs
- 1/2 cup (120ml) vegetable oil or melted butter
- 1 tsp vanilla extract
For the Cream Cheese Filling:
- 8 oz (225g) cream cheese, softened
- 1/4 cup (50g) granulated sugar
- 1 tsp vanilla extract
How Much Time Will You Need?
This recipe takes about 15 minutes to prepare, plus 18-22 minutes of baking time. After baking, allow the muffins to cool for about 5 minutes in the pan and then completely on a wire rack. In total, you’ll need about 45 minutes from start to finish to enjoy these delicious muffins!
Step-by-Step Instructions:
1. Preheat the Oven:
Begin by preheating your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the tins well with cooking spray or butter to avoid sticking.
2. Prepare the Cream Cheese Filling:
In a medium bowl, beat the softened cream cheese, sugar, and vanilla extract together using a hand mixer or a whisk until the mixture is smooth and creamy. Set this filling aside while you make the muffins.
3. Mix Dry Ingredients:
In a large mixing bowl, whisk together the flour, baking powder, baking soda, salt, and pumpkin pie spice. Make sure there are no lumps so that the ingredients are evenly distributed.
4. Mix Wet Ingredients:
In a separate bowl, combine the pumpkin puree, granulated sugar, brown sugar, eggs, oil (or melted butter), and vanilla extract. Whisk these ingredients together until smooth and well combined.
5. Combine Wet and Dry Ingredients:
Pour the wet ingredients into the bowl of dry ingredients. Stir gently using a spatula or wooden spoon just until the mixture is combined. Be careful not to overmix; a few lumps are okay!
6. Assemble the Muffins:
Using a spoon or ice cream scoop, place about 1-2 tablespoons of pumpkin batter into the bottom of each muffin cup. Then, add a teaspoon of the cream cheese filling on top of the batter. Finally, cover the cream cheese with more pumpkin batter, filling the muffin cups about 3/4 full. To create a marbled effect, you can use a knife or skewer to gently swirl the cream cheese filling into the top layer of pumpkin batter.
7. Bake the Muffins:
Place the muffin tin in the preheated oven and bake for 18-22 minutes. Check for doneness by inserting a toothpick near the edge of a muffin (making sure not to hit the cream cheese center). The toothpick should come out clean or with a few moist crumbs.
8. Cool the Muffins:
Once baked, remove the muffins from the oven and let them cool in the pan for about 5 minutes. Then, transfer the muffins to a wire rack to cool completely before serving.
9. Enjoy!
These pumpkin cheesecake muffins can be served warm or at room temperature. They can be kept in an airtight container for 2-3 days or stored in the refrigerator for up to a week. Enjoy the cozy flavors of pumpkin and cream cheese filling!

Can I Use Fresh Pumpkin Instead of Canned?
Absolutely! If you prefer fresh pumpkin, you can roast it until tender and then puree it. Make sure to drain excess moisture to avoid watery muffins.
What Can I Substitute for Vegetable Oil?
You can use melted butter for a richer flavor, or substitute with coconut oil for a slightly different taste. Applesauce is also a great alternative for a healthier, lower-fat option!
How Should I Store Leftover Muffins?
Store any leftovers in an airtight container at room temperature for up to 3 days. For longer storage, you can refrigerate them for up to a week or freeze them for up to 3 months. Just thaw at room temperature when you’re ready to enjoy!
Can I Make These Muffins Ahead of Time?
Definitely! You can prepare the batter the night before, cover it, and store it in the refrigerator. Just be sure to stir it gently before filling the muffin cups and baking in the morning!


