The most delicious healthy 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
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Pumpkin muffins are a must in our house once fall hits. Every year we kick things off with my healthy chocolate chip pumpkin muffins, which have become a reader favorite and one of the most-made muffin recipes on the blog. I usually keep a batch in the fridge for the easiest grab-and-go breakfast.

When I started working on a cream cheese version this year, I used that same pumpkin batter as the base. It’s one I’ve tested countless times over the years, so I know it bakes up moist and tender. From there, I tested different cream cheese fillings, sweetness levels, and baking times until the muffins came out with the perfect swirl and just the right amount of tang.

The ingredients stay true to how I like to bake. White whole wheat flour for a lighter, whole-grain base. Coconut oil for richness. Mashed bananas and real canned pumpkin for moisture. The bananas are what really keep these muffins soft without adding a ton of extra oil, and they help the muffins stay fresh for days.

side view close up pumpkin cream cheese muffins recipe

Pumpkin Muffin Ingredients

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

ingredients for pumpkin muffins
  • Pumpkin puree – you want canned pumpkin puree and not pumpkin pie filling. 
  • Bananas – anywhere from 2-3 ripe bananas. 
  • Coconut oil – you can substitute with a neutral oil, such as avocado oil. 
  • Honey – or maple syrup would be a great swap.
  • Eggs – large eggs, preferably at room temperature.
  • Milk – I like using whole milk but lower-fat milk will work too.
  • Vanilla extract – it will enhance the flavor.
  • White whole wheat flour – or 100% whole wheat flour is a good swap for more dense and heartier muffins. I like King Arthur brand.
  • Pumpkin pie spice – it’s a blend of cinnamon, ginger, nutmeg, and cloves.
  • Baking soda – it’s not the same as baking powder. I do not recommend a substitute.
  • Salt – to balance out the flavor.
  • Cream cheese – block cream cheese.

How to Make Pumpkin Spice Muffins

Step 1: Make the batter – combine the wet ingredients: pumpkin puree, bananas, coconut oil, honey, eggs, milk, and vanilla. You can either use a whisk or a wooden spoon to stir.

pumpkin muffin batter in bowl

Next, whisk the dry ingredients in a separate bowl: white whole wheat flour, pumpkin pie spice, baking soda, and salt. Add the dry ingredients to the wet and stir to combine. Do not overmix. It’s okay to have some lumps.

Step 2: Make the filling – whisk together the cream cheese and honey until smooth. You want the cream cheese to be softened at room temperature. To quickly soften the cream cheese, simply add to a bowl and microwave for 30-40 seconds.

cream cheese filling in a bowl

Step 3: Assemble the muffins – drop about 2 tablespoons of the batter into greased muffin cups. You want just enough batter to 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 adding the batter. Cover with the remaining batter to fill the muffin cups to the top. Some filling may poke out and that’s okay. 

pumpkin muffin batter in a muffin pan

Step 4: Bake the muffins – bake 18-20 minutes in a preheated 400 F oven. To check for doneness, insert a toothpick into the cake part of the muffin (not into the cream cheese filling) and if it comes out clean then the muffins are ready.

Step 5: Cool the muffins – place the muffin pan on a cooling rack to cool. Make sure you give the muffins enough time to cool before removing them from the pan. They’re going to be very delicate until they cool down. The filling will also firm up as the muffins cool. 

Pumpkin Muffin Variations

Switch up the muffins with any of these delicious add-ins. After you combine the wet ingredients with the dry, gently fold in up to ½ cup of the desired add-in. 

  • Chocolate chips
  • Chopped nuts – walnuts or pecans
  • Dried cranberries
  • Raisins

How to Store Cream Cheese Pumpkin Muffins

Muffins taste best on the same day, though they may be covered tightly and stored in the refrigerator for up to 1 week. They will slightly firm up once refrigerated but you can rewarm them in a microwave for about 30 seconds.

These muffins also freeze well in a freezer-safe bag for up to 3 months. Thaw overnight in the refrigerator and if desired, rewarm in the microwave.

pumpkin muffins on cooling rack

What Can I Co with Canned Pumpkin?

Here are some great ideas to use up leftover canned pumpkin puree:

Best Pumpkin Muffins FAQs

What is the secret to a moist muffin?

For this recipe the pumpkin puree and ripe bananas do all the work. They keep the muffins soft and tender without needing extra oil. Just be sure not to overmix the batter so the crumb stays light.

Are Pumpkin Muffins healthy?

These muffins are a healthier option compared to most. They use white whole wheat flour, real pumpkin puree, and bananas for natural sweetness. They still feel like a treat but with more wholesome ingredients than a typical bakery muffin.

More Muffin Recipes

Peach Muffins With Fresh Peaches

Banana Carrot Muffins

Healthy Banana Blueberry Muffins

Healthy Chocolate Chip Pumpkin 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

Best Pumpkin Muffins

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

Description

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

Ingredients

Units Scale
  • 1 cup canned pumpkin puree
  • 1 cup mashed ripe bananas, about 2 medium
  • ⅓ cup melted coconut oil (use refined for less coconut taste)
  • ½ cup honey
  • 2 large eggs
  • ¼ cup milk
  • 1 tsp. vanilla extract
  • 1 ¾ cups white whole wheat flour
  • 2 tsp. pumpkin pie spice
  • 1 tsp. baking soda
  • ½ 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.
  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.

Notes

  • 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.

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