Better Than a Bakery: Cream Cheese Filled Pumpkin Muffins with Cinnamon Sugar Tops

When fall arrives and the leaves start to turn, nothing feels quite as cozy as the scent of pumpkin spice wafting through your kitchen. These Cream Cheese Filled Pumpkin Muffins bring that classic autumn warmth soft, moist, spiced pumpkin muffin batter hugging a sweet cream cheese center, finished with a cinnamon sugar crust that crackles just right. They’re the muffin version of your favorite pumpkin cheesecake, wrapped in a handheld treat you’ll want to bake on repeat.

What Is a Pumpkin Muffin with Cream Cheese Filling?
This recipe combines a moist and tender pumpkin muffin made with real pumpkin purée and warm spices, with a hidden core of sweetened cream cheese. As they bake, the filling melts into a creamy center, while the tops develop a golden crust thanks to a cinnamon sugar sprinkle. These muffins are bakery-style in appearance and flavor but surprisingly simple to make at home.

this Recipe

Why You’ll Fall in Love with This Recipe
These muffins are everything you want in a fall treat cozy, creamy, moist, and spiced just right. The cream cheese filling adds that irresistible tang and richness, while the cinnamon sugar topping adds the perfect contrast. They stay moist for days, freeze well, and work beautifully for breakfast, dessert, or afternoon snacks. Plus, the aroma alone is enough to make you feel like you’re wrapped in a fall candle.

How Does It Taste?
The muffin itself is light yet moist, with a strong pumpkin spice profile cinnamon, nutmeg, clove, and ginger come through beautifully. The cream cheese center is sweet but tangy and adds a luscious richness to every bite. The top is slightly crisp from the cinnamon sugar, making every texture crunchy, soft, and creamy present in one bite.

Health & Ingredient Benefits
Pumpkin is naturally high in vitamin A, fiber, and antioxidants. Using real pumpkin purée (not pie filling) keeps the muffins moist without excess fat. Cream cheese provides protein and calcium, while cinnamon and spices add anti-inflammatory benefits. If you’re mindful about ingredients, you can easily swap in whole wheat flour, low-fat cream cheese, or coconut sugar without losing the integrity of the muffin.

Ingredients You’ll Need
For the muffins:
1 3/4 cups all-purpose flour
1 tsp baking soda
1/2 tsp salt
2 tsp ground cinnamon
1/2 tsp ground nutmeg
1/2 tsp ground ginger
1/4 tsp ground cloves
1 cup pumpkin purée
1/2 cup brown sugar
1/2 cup granulated sugar
1/2 cup vegetable oil
2 large eggs
1 tsp vanilla extract

For the cream cheese filling:
8 oz cream cheese, softened
1/4 cup granulated sugar
1/2 tsp vanilla extract

For the cinnamon sugar topping:
2 tbsp granulated sugar
1/2 tsp ground cinnamon

Tools You’ll Need
12-cup muffin tin
Cupcake or muffin liners
Electric hand or stand mixer
Mixing bowls
Spatula
Whisk
Cookie scoop or spoon
Cooling rack

Optional Substitutions & Additions
Use low-fat or dairy-free cream cheese
Replace brown sugar with coconut sugar or maple sugar
Add chopped pecans or walnuts for texture
Mix in mini chocolate chips to the batter
Use a gluten-free flour blend for a GF version

How to Make

1. Preheat oven to 350°F (175°C) and line a muffin tin with paper liners.
2. Make the cream cheese filling: Beat softened cream cheese with sugar and vanilla until smooth. Set aside.
3. Whisk dry ingredients: In a bowl, combine flour, baking soda, salt, and spices.
4. Mix wet ingredients: In another bowl, stir pumpkin purée, both sugars, oil, eggs, and vanilla.
5. Combine wet and dry ingredients just until no flour remains do not overmix.
6. Fill muffin cups: Spoon a tablespoon of batter into each liner, then a heaping teaspoon of cream cheese mixture, followed by more batter to cover.
7. Swirl tops slightly with a toothpick and sprinkle with cinnamon sugar.
8. Bake for 18–20 minutes or until tops spring back and a toothpick in the edge (not center) comes out clean.
9. Cool in pan for 5 minutes, then transfer to a wire rack. Enjoy warm or at room temp.

What to Serve With
These muffins pair beautifully with coffee, chai lattes, hot cider, or a glass of milk. For breakfast, add a side of fruit or yogurt. As dessert, they’re divine with a scoop of vanilla ice cream or a drizzle of caramel sauce.

Tips for Success
Use room temperature cream cheese for a smooth filling
Don’t overfill muffin cups 3/4 full is perfect
Swirl cream cheese just a little to create that marbled look
Let muffins cool slightly before peeling liners they’re tender when hot
Store in a sealed container to keep them moist

Common Mistakes to Avoid
Using pumpkin pie filling instead of pure pumpkin it’s too sweet
Skipping the swirl or underfilling cream cheese should be well-centered
Overmixing the batter, which makes muffins dense
Not fully softening cream cheese it’ll clump in the center
Overbaking, which dries them out start checking at 18 minutes

How to Store & Reheat
Store muffins in an airtight container at room temperature for 2 days, or refrigerate up to 5 days. To reheat, warm in the microwave for 10–15 seconds. You can also freeze them for up to 2 months thaw overnight in the fridge or warm directly from frozen in the microwave or oven.

Frequently Asked Questions
Can I make these ahead? Yes these are great for baking in advance and refrigerating or freezing.
Can I use a piping bag for filling? Yes it makes it even easier to portion the cream cheese.
Can I use fresh pumpkin? Absolutely just be sure to strain it well to remove excess moisture.
Can I make these into mini muffins? Yes, just reduce bake time to 10–12 minutes and watch closely.
Can I skip the cream cheese filling? Sure, but it’s what makes these muffins extra special.

Nutritional Info (approximate per muffin)
Calories: 270
Fat: 14g
Carbs: 32g
Sugar: 19g
Protein: 4g
Fiber: 2g
Sodium: 180mg

Conclusion
These Pumpkin Muffins with Cream Cheese Filling are the ultimate fall bake warm, spiced, tender, and rich without being too sweet. Whether you’re enjoying them as a cozy breakfast, a holiday brunch treat, or an after-dinner snack, they bring all the comfort of the season into one handheld delight. Make a batch (or two), because they disappear fast!

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August 18, 2025 by Melissa