The most delicious pumpkin muffins with a cream cheese filling. They’re made with whole grains and sweetened with honey. You won’t believe how moist they taste!

Love pumpkin flavor? Try our Easy Pumpkin Bread!

overhead pumpkin muffins with cream cheese this recipe

Why I Love This Recipe

Pumpkin muffins are one of the first things I want to bake once fall rolls around. I use the same pumpkin-banana batter as my chocolate chip pumpkin muffins, which has been a favorite on the blog for years, but add a lightly sweet cream cheese filling to make these extra delicious.

The banana and pumpkin keep the muffins really soft and moist, while white whole wheat flour gives them a little more staying power for breakfast. I usually keep them in the fridge and warm one up when we need something quick in the morning.

side view close up pumpkin cream cheese muffins recipe

Ingredients You’ll Need

See the recipe card for full information on ingredients and quantities.

  • Pumpkin Purée: Use 100% pure pumpkin, not pumpkin pie filling.
  • Bananas: Measure out 1 cup mashed banana, which is usually about 2 medium bananas. They add moisture and natural sweetness to the muffins.
  • White Whole Wheat Flour: It has a milder flavor than traditional whole wheat flour while still giving you a whole-grain muffin. Feel free to use plain white flour.
  • Cream Cheese: Use block-style cream cheese and soften it before mixing the filling.
  • Coconut Oil: Refined coconut oil has less coconut flavor. A neutral oil such as avocado oil also works.
ingredients for pumpkin muffins

Will the Muffins Taste Like Banana?

The banana adds moisture and a little natural sweetness. If your bananas are very ripe, you might taste a hint of banana, but the pumpkin and warm spices still come through the most.

How to Make Pumpkin Muffins with Cream Cheese

Step 1: Make the muffin batter. Whisk together the pumpkin, mashed banana, coconut oil, honey, eggs, milk, and vanilla. In a separate bowl, whisk the flour, pumpkin pie spice, baking soda, and salt. Add the dry ingredients to the wet and stir just until combined. A few lumps are fine.

pumpkin muffin batter in bowl

Step 2: Make the cream cheese filling. Stir the softened cream cheese and honey together until smooth.

cream cheese filling in a bowl

Step 3: Assemble the muffins. Add about 2 tablespoons of batter to each muffin cup, just enough to cover the bottom. Spoon a heaping tablespoon of cream cheese filling into the center, then cover with the remaining batter. It’s okay if a little filling shows at the top.

pumpkin muffin batter in a muffin pan

Step 4: Bake. Bake at 400°F for 18 to 20 minutes. Check for doneness by inserting a toothpick into the pumpkin part of the muffin, not the cream cheese center.

My Best Tips

  • Measure the banana. Use 1 cup mashed banana rather than relying on a certain number of bananas.
  • Don’t overmix. Stir the flour into the wet ingredients only until you no longer see dry streaks.
  • Use softened, not melted, cream cheese. It should be easy to stir with the honey but still thick enough to stay in the center of the muffins.
  • Don’t test through the filling. Insert your toothpick into the pumpkin portion of the muffin. The cream cheese center will stay soft even when the muffin is fully baked.
  • Let them cool before removing them from the pan. The muffins are delicate while hot, and the cream cheese center firms as they cool.
pumpkin muffins on cooling rack

Variations and Substitutions

  • Use another oil. Avocado oil or another neutral-flavored oil can be used in place of coconut oil.
  • Swap the sweetener. Maple syrup can be used instead of honey.
  • Add chocolate chips. Stir a handful into the batter before filling the muffin cups.
  • Add nuts. Chopped pecans or walnuts are a good option if you want a little crunch.
  • Use all-purpose flour. You can use all-purpose flour in place of white whole wheat flour. The muffins will be a little lighter in texture.

More Muffin Recipes

Peach Muffins With Fresh Peaches

Banana Carrot Muffins (Healthy Breakfast Muffins!)

Healthy Banana Blueberry Muffins

Pumpkin Banana Chocolate Chip Muffins

If you make this recipe, please leave a ⭐️ STAR rating and COMMENT letting us know how you liked the recipe.

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healthy pumpkin muffins on cooling rack

Healthy Pumpkin Cream Cheese Muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 4 reviews
  • Author: Katya
  • Prep Time: 10 min
  • Cook Time: 20 min
  • Total Time: 30 minutes
  • Yield: 12 1x
  • Category: Breakfast
  • Method: Baked
  • Cuisine: American
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Description

Soft and moist pumpkin muffins made with whole wheat flour, banana, and honey with a lightly sweet cream cheese filling in the center.

Ingredients

Units Scale
  • 1 cup canned pumpkin puree
  • 1 cup mashed ripe bananas, about 2 medium
  • 1/3 cup melted coconut oil (use refined for less coconut taste)
  • 1/2 cup honey
  • 2 large eggs
  • 1/4 cup milk
  • 1 tsp. vanilla extract
  • 1 3/4 cups white whole wheat flour
  • 2 tsp. pumpkin pie spice
  • 1 tsp. baking soda
  • 1/2 tsp. salt
  • Optional: pumpkin seeds

Cream Cheese Filling

  • 8 oz. block cream cheese, softened at room temperature
  • 3 Tbsp. honey

Instructions

  1. Preheat oven to 400 degrees F. Grease 12-cup muffin pan with non-stick spray. Or line the pan with paper muffin cups, and grease the cups. Set aside.
  2. To make the muffin batter: In a large bowl, combine the pumpkin puree, bananas, coconut oil, honey, eggs, milk, and vanilla extract. I like using a whisk for this step but a big wooden spoon also works.
  3. In a separate bowl, whisk together the flour, pumpkin pie spice, baking soda, and salt, and add to the pumpkin mixture. Stir with a wooden spoon just until combined. Some lumps are okay. Set aside.
  4. To make the filling: Whisk together the softened cream cheese and honey until smooth.
  5. Assemble: Drop about 2 tablespoons of the batter into each muffin cup. It should cover the bottom. Add a heaping tablespoon of the cream cheese filling. If you have leftover filling, go back and add the rest to the cups before covering with batter. Cover with the remaining batter to fill the muffin cups to the top. Some filling may poke out of the sides or out of the top. If desired, sprinkle the tops with pumpkin seeds.
  6. Bake 18-20 minutes or until toothpick inserted into the cake part of the muffin (not into the cream cheese filling) comes out clean.
  7. Place the muffin pan on a cooling rack to cool. The filling will firm up as the muffins cool. Do not try to remove muffins while they are hot. After the muffins cool, remove them from the pan.

Notes

  • Bananas: Bananas make these muffins incredibly moist and I do not recommend substituting with anything. Muffins do have a slight banana taste to them.
  • Honey: Maple syrup would be a good substitute for honey.
  • Flour: I love using King Arthur white whole wheat flour for its mild flavor. You can substitute with 100% whole wheat flour but just keep in mind the muffins will be more dense.
  • Storing Leftovers: Once cooled, store the muffins tightly covered in the refrigerator for up to 5 days. Rewarm briefly in the microwave if you prefer them warm. Freeze in a freezer-safe container for up to 3 months and thaw overnight in the refrigerator.

Nutrition

  • Serving Size: 1 muffin
  • Calories: 272
  • Sugar: 19.3 g
  • Sodium: 277.7 mg
  • Fat: 13.9 g
  • Carbohydrates: 34.7 g
  • Protein: 5.1 g
  • Cholesterol: 50.2 mg