These Pumpkin Cheesecake Muffins are sweet and filled with cozy seasonal flavor. Made with real pumpkin and a tangy cream cheese center, they’re an ideal treat for crisp autumn afternoons — and they take just 30 minutes from start to finish.
Pair these moist, delicately spiced Pumpkin Cheesecake Muffins with a warm pumpkin latte for a perfect fall snack. The muffins are soft, lightly sweetened, and have a creamy cream cheese surprise in the center that makes them feel extra special. They’re great for afternoon coffee breaks, brunch, or as a festive addition to a holiday spread.
Why make these muffins?
- Deliciously spiced pumpkin muffins with a creamy cheesecake filling.
- Simple one-bowl batter using common pantry ingredients.
- Made with whole-grain flour for extra fiber and nutrition.
- Sweetened without refined processed sugar when using maple syrup or honey.
- A nutritious way to enjoy pumpkin — rich in vitamins and antioxidants.
Ingredients used
This recipe is straightforward and uses basic pantry staples:
- Whole-grain flour. A nutritious alternative to all-purpose flour. Spelt flour works well, but any whole-grain flour may be used.
- Sweetener. Pure maple syrup is used here; honey or other liquid sweeteners can be substituted.
- Pumpkin puree. Adds natural sweetness, moisture, and flavor.
- Pumpkin spice. Use a store-bought blend or a homemade mix of cinnamon, ginger, nutmeg, allspice and a touch of cloves.
Other pantry items:
- Eggs (room temperature)
- Vanilla extract
- Baking soda
- Pinch of salt
- Extra virgin coconut oil (melted and cooled)
- Muscovado or brown sugar (optional, for depth of flavor)
- Cream cheese (for the filling)
How to make Pumpkin Cheesecake Muffins
Prep takes about 10 minutes; bake time is 20–22 minutes. Follow these simple steps for reliably moist muffins with a creamy center.
Equipment
- Measuring cups
- Mixing bowls
- Whisk and spatula
- 12-cup muffin tin and liners
Step-by-step instructions
- Step 1 – Prepare: Preheat oven to 190°C/375°F. Line a 12-cup muffin tin with liners. Melt coconut oil and let it cool slightly.
- Step 2 – Make the filling: In a small bowl, whisk cream cheese with the egg yolk and vanilla until smooth. Set aside.
- Step 3 – Mix dry ingredients: In a medium bowl, combine flour, pumpkin spice, baking soda, and salt.
- Step 4 – Mix wet ingredients: In a large bowl, whisk eggs with melted coconut oil, pumpkin puree, maple syrup, and vanilla until combined.
- Step 5 – Combine and bake: Fold the dry ingredients into the wet mixture just until combined. Gently fold in the muscovado sugar if using. Spoon batter into liners, filling each about 3/4 full. Add about a teaspoon of cream cheese filling to the center of each muffin and swirl gently with a toothpick. Bake 20–22 minutes or until a toothpick inserted into the muffin (not the cream cheese) comes out clean. Cool before serving.
Substitutions
- Flour: Swap spelt for any whole-grain flour, or use all-purpose flour 1:1.
- Sweetener: Use honey, date syrup, or molasses (these may darken the muffins).
- Fat: Replace coconut oil with avocado oil or butter (if using salted butter, omit added salt).
- Sugar: Muscovado can be swapped for brown sugar or coconut sugar.
- Pumpkin spice: For 1 tsp pumpkin pie spice, use 3/4 tsp cinnamon + 1/4 tsp ginger plus a pinch of nutmeg, allspice and cloves.
Storage tips
- Counter: Keep cooled muffins in an airtight container for 3–4 days.
- Refrigerator: Store up to one week in an airtight container.
- Freezing: Freeze muffins in a zip-lock bag for up to 3 months. Thaw at room temperature. Warm gently in the microwave before serving if desired.
Recipe tips
- Fold batter gently with a spatula and avoid over-mixing to keep muffins light and tender.
- Check doneness with a toothpick in the muffin (avoid the cream cheese center); it should come out clean or with a few crumbs.
- Use room-temperature eggs for a smoother batter — set them out before baking or warm briefly under running water.
- When substituting coconut oil with salted butter, omit additional salt from the recipe.
- Liquid sweeteners like honey or maple syrup work best; stevia or other low-carb sweeteners can be used for lower-sugar versions.
Recipe variations
- Add dried fruit such as cranberries or raisins.
- Stir in chopped nuts like walnuts, pecans, or hazelnuts for crunch.
- Protein boost: Replace 1/4 cup flour with one scoop vanilla protein powder and reduce vanilla and sweetener slightly.
- Gluten-free option: Use a gluten-free flour blend in place of whole-grain flour.
Recipe
Pumpkin Cheesecake Muffins
Servings: 12 muffins | Prep: 10 mins | Cook: 20 mins | Total: 30 mins
Ingredients
For the muffins:
- 1 ¾ cups whole wheat or whole-grain flour
- 1 teaspoon pumpkin spice mix
- 1 teaspoon baking soda
- ½ teaspoon salt
- 2 large eggs
- 1 cup pumpkin puree
- ½ cup melted and cooled extra virgin coconut oil
- ½ cup pure maple syrup
- 1 teaspoon vanilla extract
- 1 tablespoon muscovado sugar (optional)
For the filling:
- 1 cup cream cheese
- 1 egg yolk
- 1 teaspoon vanilla extract
Instructions
- Preheat oven to 190°C/375°F and line a 12-cup muffin tin with liners.
- In a small bowl, whisk together cream cheese, egg yolk and vanilla for the filling. Set aside.
- In a medium bowl, combine flour, pumpkin spice, baking soda and salt.
- In a large bowl, whisk eggs with melted coconut oil, pumpkin puree, maple syrup and vanilla until smooth.
- Fold dry ingredients into wet just until combined. If using, fold in the muscovado sugar gently.
- Spoon batter into liners, filling each about 3/4 full. Add a teaspoon of cream cheese filling to each muffin and swirl gently with a toothpick.
- Bake 20–22 minutes, or until a toothpick inserted into the muffin (not the filling) comes out clean. Cool before serving.
Notes
Makes 12 muffins. Suggested serving size is one muffin. Nutritional estimates vary by ingredient brands and measurements.
Nutrition (per muffin, approximate)
Calories: 243 kcal | Carbohydrates: 26 g | Protein: 5 g | Fat: 14 g | Fiber: 2 g | Sugar: 11 g
Originally published September 2017; updated with small changes and improvements.
More recipes to try
Pumpkin Bars-
Pumpkin Loaf Cake
-
Pumpkin Chocolate Chip Bread
-
Pumpkin Roll Cake
