Apple Pie Cream Cheese Muffins

Apple Pie Cream Cheese Muffins

Recipe inspiration can come from some funny places. I decided to make these muffins after buying some cute red cupcake liners from Target. I just knew I had to put something with apple in them (and it helped that I had basket full of apples waiting for me at home). I promise I’ll move on to something else besides apples after this, but I had to share this recipe because I was so happy with how these turned out.

It’s a little hard to tell from the pictures what exactly these muffins are since many of the components are a similar color, so let me just describe it for you: it starts with a graham cracker crust on the bottom (like a little pie!), the muffin is a spiced applesauce cake with cinnamon cream cheese in the middle and it’s all topped with caramelized apples. Basically, I was torn between making a pie or cake, so I decided to combine them!

Apple Pie Cream Cheese Muffins

I got the idea for adding the graham cracker crust from a different recipe I saw on Pinterest last month and it works spectacularly well with the spiced apple cake. It’s almost like an upside-down streusel, because it adds the same kind of crunchy (but still soft and easy to bite through) texture but it’s on the bottom of the muffin instead of the top. It’s so good! I want to put a graham cracker crust on all my muffins from now on. I was this close to actually putting a streusel on top, too, but decided that simple caramelized apples would be much better. These muffins are sweet enough, they don’t need an extra sugary topping.

Apple Pie Cream Cheese Muffins

Muffin ingredients

This recipe has a lot of ingredients and components, but don’t be intimidated! You will have most of these ingredients in your kitchen already and each component is very simple and easy to prepare. Everyone knows how to make graham cracker crust, right? (If you don’t, it’s time to learn!) The muffins are based on my tried and true applesauce bread recipe, which I modified to be a bit healthier by adding some whole wheat flour and subbing some nutrient-rich maple syrup for the sugar. To caramelize the apples you just need to cook them on the stove with a little butter, cinnamon and sugar until they’re nice and tender; it takes less than 10 minutes. While the apples cook, you can (literally and figuratively) whip up the cream cheese filling in a mixer.

I just find these apple pie muffins so satisfying. To take a bite and get all the flavors from graham cracker crumbs, apple pie spices, cream cheese and caramelized apples just makes me happy. One muffin with all my favorite things! They’re perfect for breakfast or dessert on another lovely fall day.

Apple Pie Cream Cheese Muffins

Apple Pie Cream Cheese Muffins

from Back to the Cutting Board

Breakfast, Dessert | Yield: 16-18 muffins
Prep time: 45 min | Cook time: 25 min | Total time: 1 hour 10 min


Cinnamon Graham Cracker Crust

  • 1 cup (5 oz.) finely ground graham cracker crumbs (I used low-fat cinnamon graham crackers)
  • 2 tbsp. (.9 oz) sugar
  • 1/2 tsp. (1.4 g) cinnamon (optional)
  • 4 tbsp. (2 oz. – 1/2 stick) unsalted butter, melted

Apple Topping

  • 2 large tart apples
  • 2 tbsp. (1 oz. – 1/4 stick) unsalted butter (softened)
  • 2 tbsp. (.9 oz) sugar
  • 1 tsp. (2.8 g) cinnamon

Cinnamon Cream Cheese Filling

  • 4 oz. cream cheese, softened (I used 1/3 less fat)
  • 1 egg yolk (optional)
  • 1/4 cup (1.8 oz) sugar
  • 1 1/2 tsp. (4.2 g) cinnamon
  • 1/4 tsp. (1 g) vanilla


  • 1/2 cup (4 oz. – 1 stick) unsalted butter (softened)
  • 1/2 cup (3.5 oz) sugar
  • 2 eggs
  • 1/2 tsp. (2 g) vanilla
  • 1 cup (5 oz) all-purpose flour
  • 1 cup (3.4 oz) whole wheat pastry flour(or twice-sifted whole wheat flour)
  • 1 tsp. (6.7 g) salt
  • 1 tsp. (4.9 g) baking powder
  • 1/2 tsp. (2.5 g) baking soda
  • 1/2 tsp. (1.4 g) cinnamon
  • 1/2 tsp. (2 g) nutmeg
  • 1/8 tsp. (.2 g) cardamom (optional)
  • 1 cup (8 oz) unsweetened applesauce
  • 1/3 cup (3.6 oz) maple syrup


  1. Preheat oven to 350 degrees (F). Grease two muffin pans (only the top edge of each cup needs to be greased/sprayed) and fill with 18 cupcake liners.
  2. In a medium bowl, mix together the graham cracker crumbs, sugar and cinnamon. Pour in the melted butter and stir until well distributed. Spoon two heaping teaspoons into each muffin cup and evenly press the crumbs into the bottom.
  3. Apples

    Peel and core the apples. Cut them into quarters and then slice each quarter into thirds. Cut each slice into 1/2-inch pieces. You’ll wind up with a bunch of little triangular pieces of apple.

  4. Apple topping

    In a large skillet over medium-high heat, melt the butter, sugar, and cinnamon. When the mixture starts to bubble add the apple pieces and toss to coat. Cook for 1 minute without stirring. Stir again and cook for about 6 more minutes, stirring every minute or so, until tender and caramelized. You may need to lower the heat a bit while they cook, stop cooking if the apples look dry or start burning. Set aside to cool.

  5. While the apples are cooking, beat the cream cheese on medium speed until creamy. Add in the egg yolk and mix well. Gradually add the sugar, cinnamon and vanilla and beat until well blended. Set aside. (If you only have one bowl for your mixer (like me) you’ll need to transfer this to another bowl and wash the mixer bowl so you can use it to make the muffins.)
  6. In a mixer bowl cream the butter, gradually adding the sugar, until light and fluffy. Add eggs and beat until well combined.
  7. In a separate bowl combine the flours, salt, baking powder, baking soda and spices.
  8. In another bowl mix the applesauce and the maple syrup.
  9. On the lowest speed mix in half the dry mixture with the butter mixture. Then mix in 1/2 of applesauce mixture. Repeat with remaining dry mixture and remaining applesauce, mixing after each.
  10. Cream cheese filling

    Fill each muffin cup about halfway. Add a rounded teaspoon of the cream cheese in the middle of each muffin cup. Top with the remaining batter (about two tablespoons).

  11. Apple topping

    Gently spoon a few teaspoons of the apples on top of each muffin.

  12. Bake for 25-30 minutes or until the edges start to brown and a toothpick comes out clean. Cool 10 minutes in the pan, then transfer the muffins to a wire rack to cool completely.

Apple Pie Cream Cheese Muffins

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  1. wow that sounds like a killer combo!

  2. What a great muffin you have here! perfect for fall.

  3. Those muffins look so good!

  4. Yum, these muffins look so tasty. You can’t go wrong with cream cheese and cinnamon. Thanks for sharing!

  5. I’m such a muffin fan & cream cheese is my most favorite ingredient. Love apples too – these gotta be some awesome bites of perfection. Thanks for sharing your amazing photos. I wanna be just like you when I grow up.

  6. in step #9 the word “pumpkin” was used?? Please clarify!

  7. I don’t have any whole wheat flour, would only all purpose do the job?

    • Yep, all-purpose is totally fine. That’s what the original recipe calls for, I’ve just been trying to incorporate some whole grain flour in recipes whenever I can.

  8. Ok. Thanks!!! I made them and they came out great! Only I didn’t have enough batter for all 18, I could only make 12. I did have enough graham cracker mixture and cream cheese mixture for 18 though. Maybe I filled them up too much. Oh well, they are so good and the kids love them!

  9. Graham cracker crust in a muffin? Genius!

    Maria xx

  10. This looks absolutely divine. I’m totally into apple flavors this fall 🙂

  11. Your muffins look so good and moist! I bet your house smelled wonderful as they were baking!