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A partially unwrapped Whole Wheat Pumpkin Cheesecake Muffin on a white wooden background.

Whole Wheat Pumpkin Cheesecake Muffins

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  • Author: Bailey Sissom


Whole Wheat Chocolate Chip Pumpkin Cheesecake Muffins are naturally sweetened, moist, delicious and wholesome. The perfect healthier homemade snack or breakfast option!



For The Pumpkin Muffins:

  • 1/3 cup melted coconut oil
  • 1/2 cup maple syrup
  • 2 eggs
  • 1 cup pure pumpkin puree
  • 1/4 cup whole milk
  • 1 tsp. vanilla
  • 1 tsp. baking powder
  • 1/2 tsp. salt
  • 1 1/2 tsp. pumpkin pie spice
  • 1 3/4 cup whole-wheat flour
  • 1/3 cup old fashioned oats
  • 1/3 cup mini chocolate chips

For The Cheesecake Topping:

  • (1) 8 oz. container cream cheese (room temperature)
  • 1/3 cup coconut sugar (you can sub brown sugar)
  • 1 egg
  • 1 tsp. vanilla extract
  • mini chocolate chips (for sprinkling on top of muffins)


  1. Heat the oven to 350 degrees and line the cups of a muffin tin with paper liners.
  2. In a large mixing bowl, add the coconut oil, maple syrup, eggs, pumpkin puree, milk and vanilla. Whisk until fully combined.
  3. In a second mixing bowl, combine the baking powder, salt, pumpkin pie spice, whole wheat flour and oats. Mix to combine.
  4. Carefully pour the wet ingredients into the dry and use a wooden spoon to gently combine. Do not over-mix. Fold in the chocolate chips. Set pumpkin batter aside.
  5. To the base of a stand mixer (or mixing bowl - if using a handheld mixer) add cream cheese, coconut sugar, egg and vanilla. Beat until fully combined and smooth.
  6. Fill each muffin cup 3/4 full with the pumpkin batter. Then, use the same scoop to add an additional 1-2 Tbs. of cream cheese topping to each muffin.
  7. Bake for 25-30 minutes or until an inserted toothpick comes out clean. Allow muffins to cool for 5-10 minutes before removing to a cooling rack. Store cooked muffins in the refrigerator.