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Butternut Squash Muffins with Cream Cheese Filling

butternut squash muffin with cream cheese filling toasted butternut squash seeds

Butternut Squash in a muffin? I’m in! Made with my simple Roasted Butternut Squash Puree recipe, these moist muffins are the perfect addition to a morning cup of coffee on a cold day. The butternut squash gives these muffins a natural buttery flavor without adding any butter! These little gems can be stuffed with my delicious cream cheese filling…or without. Ask anyone who knows me and they will confirm that I love sweet treats (seconds and thirds please!). I also love it when I can have a sweet treat that comes with a little less guilt so I have listed some alternatives to this recipe if you are looking for something on the lighter side.

First, here are some helpful baking tips

When measuring out the flour I recommend using a spoon. Do not scoop and pack the measuring cup full because you will end up with more flour than you need. You would be surprised how much flour you will save and your baked goods will come out fluffier!

Mix your wet and dry in separate bowls before combining them. The only dry ingredient I recommend adding to wet is sugar because it will dissolve faster.

portioning butternut squash muffin batter

Use a ladle to measure your batter to ensure to are adding the same amount of batter to each cup.

How to add filling to a muffin you ask?

filling being piped into bottom of butternut squash muffin

Adding a filling into muffins is easier then you think. I recommend inserting the tip into the bottom rather than the top unless you are going to top with frosting in order to hide the hole. Be sure to hold the muffin with one hand and the piping bag with the other, squeeze the piping bag until you feel the muffin start to expand (but not break apart so be careful). If you’re not even sure how to use a piping bag in the first place then check out the editorial from the blog Kitchn that is super helpful.

Recipe Alternatives

Before we dive in I just want for you to keep in mind that I have not tested some of these alternatives within this particular recipe. I am going off of what has worked for me in the past. I would love to hear feedback from anyone that tries either these substitutions of some of their own.

  • If at all possible do not substitute eggs in this recipe but if you absolutely cannot have them then add an extra 1/2 cup of the butternut squash puree
  • The whole milk is optional but I recommend it because it adds extra moisture to the end result. You may substitute whole milk for coconut milk, just make sure the coconut milk has a moderate amount of fat. Sorry but no almond milk alternative
  • Normally I like to use melted butter for my muffin recipes but since the butternut squash gives these muffins that rich flavor I omit it for canola BUT by all means, you may substitute with butter measure for measure
  • For less saturated fat in the filling, a simple substitute for cream cheese is a Neufchatel cheese measure for measure. You won’t tell the difference!
  • Finally the flour…If you don’t mind a more dense muffin then you can substitute half the all-purpose for whole wheat but I would not go any higher than that.
  • You can cut down on the sugar or completely cut it out in place of 3/4 cup unsweetened applesauce or mashed bananas


Butternut Squash Muffins with Cream Cheese Filling

  • Author: Kristin
  • Prep Time: 1 hour
  • Cook Time: 25 minutes
  • Total Time: 1 hour 25 minutes
  • Yield: 6 large muffins 1x
  • Category: Muffins



Muffin Batter

 Dry Ingredients

  • 3 1/2 cups All Purpose flour
  • 2 teaspoons baking soda
  • 1 teaspoon kosher salt
  • 1/2 teaspoon baking powder
  • 1 1/2 teaspoon ground cinnamon
  • 1 1/2 cups chopped walnuts
  • 1 cup raisins

Wet Ingredients

  • 1 1/2 cups Roasted Butternut Squash Puree, see recipe here
  • 1 cup granulated sugar
  • 2 eggs large
  • 2/3 cup canola oil or unsalted butter
  • 2/3 cup whole milk(optional)

Cream Cheese filling (optional)

  • 1 8oz block cream or Neufchatel cheese
  • 1/4 milk
  • 1 tbsp confectioners sugar

Butterscotch Sauce topping (optional)

  • 4 tablespoons unsalted butter
  • 6 tablespoons light brown sugar
  • 3 tablespoons heavy cream
  • 1/4 teaspoon salt



    1. Pre heat conventional oven to 350 degrees.
    2. Combine all dry ingredients excluding walnuts and raisins, into bowl and whisk together, set aside.
    3. In another bowl combine oil and squash puree. Slowly add milk and eggs. This may be done by hand using a whisk but if you choose to use an electric mixer set on low speed.
    4. Slowly add the wet ingredients to dry and mix until incorporated. Add 1 cup of the chopped walnuts and all the raisins. Fold in.
    5. Spray your 6 cup muffin pan with pan coating (I prefer canola). Fill each cup 3/4 of the way with batter.
    6. Place in oven for 25 minutes. Insert a tooth pick into middle of muffin, if it comes out clean they are done. Let rest for 10 minutes before removing from pan.
    7. For the cream cheese filling a hand mixer or Kitchen Aid mixer works best. Beat cream cheese on medium high speed until softened. Slowly add the milk and sugar. Once ingredients are mixed, beat on high until fluffy (use the whisk attachment if using a Kitchen Aid).
    8. Place cream cheese filling into pipping bag fitted with a large round tip. If you aren’t sure how to use a piping bag (or even what it is) I like this tutorial from Kitchn.
    9. Once the muffins have cooled down, holding the muffin upside down in one hand and the cream cheese filled piping bag in another, insert tip into bottom of muffin about 1/2″ and squeeze bag until you feel muffin expand. 
    10. To make the butter sauce topping place a small sauce pan over medium heat and melt the butter. Add the brown sugar, cream and salt. Using a rubber spatula or whisk, bring to a light boil constintly stirring the ingredients until they are completely incorporated and the sauce starts to thicken.
    11. Drizzle sauce on top of muffins and garnish with the remaining walnuts. If you decided to toast off the squash seeds those can be used as well.


If you omit the sugar, filling and topping, these make an excellent dinner bread!

Baking times may vary slightly due to many circumstasnces including elevation or your oven make and model. Do not open oven until timer goes off and do not leave oven light on, that raises the temperature of the oven!

Keywords: butternut squash muffins with cream cheese filling, butternut squash muffins

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