Gluten-Free Applesauce Mini Muffins

I have been baking my two-and-a-half year old muffins for his preschool lunches. For so long I relied on sunflower seed butter sandwiches, but after an enlarged adenoids diagnosis, in order to reduce the inflammation, I removed gluten and dairy from his diet. In combination with his picky eating, and school allergen restrictions, figuring out what to send to school posed challenging. Mini muffins seemed to do the trick.

Last week, he came down with a 48-hour stomach bug, and his appetite was thrown off. I had some applesauce in the fridge, and decided to make another batch of muffins to get something on his stomach. Applesauce is part of the BRAT diet, and has been shown to soothe stomach upset. With excess batter, I was able to make both mini and regular sized muffins, so know that this recipe is for adults and kids alike. They are also free of gluten, dairy, nuts, refined sugar, oil, and soy, so not only are they allergen-friendly, but also safe to take into schools.

gluten-free applesauce muffins

Planning and prep

What I love about these muffins is that there is not much planning and prep. With banana muffins, you have to ensure you have ripe bananas on hand; for this recipe, all it takes is some store-bought applesauce. I typically advise letting the batter rest before baking, but with the presence of eggs, whether you let the batter rest or not shouldn’t affect rise too much.

gluten-free applesauce muffins
gluten-free applesauce muffins

Gluten-Free Applesauce Mini Muffins

A basic muffin recipe for kids or adults. Low in sugar but high in satiation, these muffins make a great snack or breakfast on the go. They are free of gluten, dairy, nuts, refined sugar, soy, and oil.
Prep Time 15 minutes
Cook Time 15 minutes
Cooling Time 1 hour
Total Time 1 hour 30 minutes
Course Breakfast
Servings 36 muffins


  • mini muffin tin or regular muffin tin; see note
  • Stand mixer or hand beater
  • Mixing bowls


  • 2 eggs beaten
  • cup unsweetened applesauce
  • ½ cup dairy-free milk I used oat milk; see note
  • ½ cup sunflower seed butter
  • 1 teaspoon vanilla extract
  • 1 cup oat flour
  • 1 cup brown rice flour
  • ¾ cup coconut sugar
  • 1 teaspoon baking powder
  • 1 teaspoon cinnamon
  • ½ teaspoon baking soda
  • ¼ teaspoon sea salt


  • Preheat the oven to 350 degrees. Line a mini muffin tin with muffin liners. You can also use a regular muffin tin, but bake time will vary. See note.
  • In a large mixing bowl, whisk together the eggs, applesauce, milk, sunflower seed butter, and vanilla extract until creamy.
  • In a separate large bowl, or bowl of a stand mixer, combine the oat flour, brown rice flour, coconut sugar, baking powder, cinnamon, baking soda, and sea salt. Stir. Pour the wet ingredients into the bowl with the flour mixture and beat until a batter is formed.
  • Transfer the batter to the muffin tin, filling each one to the top. Baking for 14 to 16 minutes, or until a toothpick inserted comes out clean. allow the muffins to cool in the muffin tin, about 30 minutes to 1 hour.


For regular muffins: bake 22 to 25 minutes until a toothpick inserted comes out clean
I used oat milk because I wanted these muffins to be safe to pack for my son’s preschool. The muffins won’t be nut-free if you use a nut milk. 
Keep muffins in an airtight container in the refrigerator for up to 1 week. They can be frozen for up to 1 year. 
Keyword Dairy-free, Gluten-free, Nut-free, Oil-free, Soy-free, Tree Nut-free
gluten-free applesauce mini muffins