close-up shot of a pumpkin muffin with a bite taken out of it to reveal a cream cheese filling

Soaked Pumpkin Cream Cheese Muffins

With cream cheese filling to make this pumpkin muffin recipe fancy even though it's super easy, and applesauce for moisture and reduced sugar, you can't get any better than this. These soaked pumpkin muffins are healthy enough to eat for breakfast!

Course Breads, Breakfast, Dessert, Snack
Cuisine American, Traditional
Prep Time 20 minutes
Cook Time 25 minutes
Soaking Time 12 hours
Total Time 12 hours 45 minutes
Servings 20 muffins
Calories 198 kcal
Author Mary Harp


For the pumpkin muffins:

For the cream cheese filling:


  1. Mix together flour, milk, and raw apple cider vinegar in a large bowl.
    clear glass bowl of batter for muffins that is soaking overnight for increased digestibility and nutrition
  2. Cover and let soak overnight, up to 24 hours.
  3. Preheat oven to 350 degrees Fahrenheit.
  4. In a separate medium-sized bowl, whisk together eggs, pumpkin, applesauce, sweetener, baking soda, spices, and salt. Slowly add melted coconut oil to mixture, whisking in slowly.
  5. Add pumpkin mixture to the soaked flour mixture.
    large glass mixing bowl with pumpkin muffin batter and a whisk
  6. Mix until smooth. It may take a little time and elbow grease to make sure everything is incorporated thoroughly. This is simply the nature of soaked muffins. If you have one, use a stand mixer.
  7. Combine cream cheese, maple syrup, and vanilla extract in a small bowl.
  8. Beat together until smooth with an electric hand mixer.
    electric hand mixer beating a mixture of cream cheese, vanilla extract, and maple syrup to make cream cheese filling
  9. Transfer to a piping bag or gallon Ziploc bag, seal, and cut a hole in the tip.
    hand holding a Ziploc bag filled with cream cheese filling, ready to be piped
  10. Fill a muffin tin with paper liners.
  11. Fill each muffin cup almost to the top with muffin batter.
    muffin tin filled with pumpkin muffin batter in muffin cups, with Ziploc bag piping cream cheese filling into each of them
  12. In the center of each muffin cup, insert the piping bag and fill with cream cheese filling. Make sure some filling is showing on top of each muffin.
    a muffin tin full of pumpkin muffin batter and cream cheese filling, ready to be baked
  13. Bake for 20 to 25 minutes. Check them a minute or two early to check for doneness – don’t overcook. Test the cakey part of the muffin with a toothpick until it comes out almost clean.
  14. Allow to cool for several minutes before enjoying.
    close-up shot of a pumpkin muffin with a bite taken out of it to reveal a pocket of cream cheese filling, with cinnaon sticks and other muffins in the background
Nutrition Facts
Soaked Pumpkin Cream Cheese Muffins
Amount Per Serving (1 muffin)
Calories 198 Calories from Fat 90
% Daily Value*
Fat 10g15%
Saturated Fat 7g44%
Cholesterol 30mg10%
Sodium 275mg12%
Potassium 125mg4%
Carbohydrates 24g8%
Fiber 1g4%
Sugar 15g17%
Protein 3g6%
Vitamin A 207IU4%
Vitamin C 1mg1%
Calcium 48mg5%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.