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two gluten free apple muffins stacked on a white plate

Gluten-Free Applesauce Muffins

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5 from 1 review

  • Author: Emily Dixon, Sweets & Thank You
  • Total Time: 33 minutes
  • Yield: 12 muffins 1x
  • Diet: Gluten Free


Soft, fluffy gluten-free apple muffins made with applesauce, warm spices, and a yummy cinnamon-sugar topping you won’t want to miss!



Dry Ingredients:

  • 1 3/4 cup (210 grams) measure for measure gluten-free flour
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 1/4 teaspoons cinnamon
  • 1/2 teaspoon ground nutmeg
  • 1/4 teaspoon ground cloves

Wet Ingredients:

  • 1/2 cup oil (canola oil, vegetable oil; or avocado oil)
  • 1/2 cup (100 grams) sugar
  • 1/4 cup (50 grams) light brown sugar
  • 1 1/2 cups unsweetened applesauce
  • 3 large eggs
  • Optional: 1 cup grated apple or chopped nuts (like pecans or walnuts)

Optional Cinnamon-Sugar Topping*

  • 1 Tablespoon melted butter
  • 2 teaspoons ground cinnamon
  • 1/4 cup (50 grams) granulated sugar
  • 2 Tablespoons (15 grams) gluten-free measure-for-measure flour


  1. Preheat & Prep. Start by preheating the oven to 400 degrees F. Line a 12-cup metal muffin pan with parchment liners or grease each muffin cup.
  2. Combine The Dry Ingredients. In a medium bowl, combine gluten-free flour blend, baking soda, salt, cinnamon, nutmeg, and cloves. Whisk to combine well.
  3. Mix Wet Ingredients. In a large bowl, combine sugar, brown sugar, and oil. Whisk to combine. Mix in applesauce, the mix in the eggs one at a time. 
  4. Finish The Batter. Add the dry ingredients to the wet ingredients and stir until just combined. If desired, fold in 1 cup grated apple or chopped nuts. 
  5. Let The Batter Rest. For best results, let the batter rest for 30-60 minutes. This will give your muffins a MUCH bigger rise and is worth the wait!
  6. Mix Up Cinnamon-Sugar Mixture. In a small bowl, combine melted butter, cinnamon, sugar, and flour. Stir with a fork until everything is well combined and the butter is coating all the dry crumbs. It’ll be thick and powdery. 
  7. Scoop The Batter. After letting the batter rest, gently use an ice cream scoop to spoon about 1/4 cup of batter into each muffin cup, filling each muffin cup almost up to the top of the parchment liner. (Depending on how much the batter has expanded, you may end up having 1-2 muffins extra batter. You can bake these in a second batch.) Try to be gentle here so you don’t deflate the batter. Sprinkle tops the muffins with cinnamon sugar mixture. 
  8. Bake & Cool. Put the muffins in the oven and bake 5 minutes at 400 degrees. Reduce the temperature to 350 degrees and continue baking for 10-14 minutes, or until the muffins are done. The interior should reach at least 205 degrees F., the tops should spring back when gently pressed, and a toothpick inserted in the center should come out with just a few moist crumbs. Let the muffins cool 1-2 minutes in the pan, then transfer to a wire rack to cool completely.
  9. Serve & Store. Enjoy warm muffins right away, or store leftover muffins in an airtight container at room temperature up to 2 days or in the freezer up to 2 months.


*Or Try It With Streusel! 

  • In a small bowl, combine 3/4 cup (90 grams) gluten-free flour, 1/4 cup (50 grams) brown sugar, 1/4 cup (50 grams) sugar, 1 teaspoon cinnamon, and 5 Tablespoons melted butter. Stir with a fork until clumps and clusters form. 
  • Sprinkle the crumb topping over the muffin batter in each muffin cup, generously covering them and gently patting the crumb topping down a bit into the batter.
  • Prep Time: 15 minutes
  • Cook Time: 18 minutes
  • Category: Breakfast
  • Method: Oven
  • Cuisine: American
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