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healthy pumpkin muffins on cooling rack

Healthy Pumpkin Cream Cheese Muffins

  • Author: Katya
  • Prep Time: 10 min
  • Cook Time: 20 min
  • Total Time: 30 minutes
  • Yield: 12 1x
  • Category: Breakfast
  • Method: Baked
  • Cuisine: American


Truly the most delicious healthy pumpkin muffins with cream cheese filling. You won’t believe how moist they are!


  • 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


  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.
  8. Store cooled muffins in the refrigerator, tightly covered, for up to 1 week. Or freeze in a freezer-safe bag for up to 3 months.


  • Pumpkin Puree: Make sure you’re using pumpkin puree and not pumpkin pie filling.
  • 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.
  • Cream Cheese: To quickly soften the cream cheese, add to a bowl and microwave for 30-40 seconds.
  • Storing Muffins: Cooled muffins can be stored in the refrigerator for up to 1 week. When refrigerated, they will slightly firm up. If desired, warm up in a microwave before serving. I’ve left muffins out at room temperature for 1-2 days and they were okay. Just make sure to keep the muffins tightly covered so they don’t dry out. These muffins also freeze well in a freezer-safe bag for up to 3 months. Thaw overnight in the refrigerator and rewarm in the microwave if desired.

Keywords: pumpkin muffins, healthy muffins, cream cheese muffins