The Best Gluten Free Applesauce Muffins Recipe

Gluten free applesauce muffins on a tabletop and in a wire basket with a bowl of strawberries.

Looking for gluten free muffin recipes? This gluten-free applesauce muffins recipe is perfect for breakfast or as a quick after-school snack.

Make this gluten free muffin recipe the night before with unsweetened applesauce and raisins or other fun mix-ins like chocolate chips.

This is a great recipe for freezing so you always have some on hand to enjoy.

How to make gluten free muffins with applesauce

With a few substitutions, you can easily make these easy gluten-free muffins sugar-free, dairy-free, or vegan.

1. Preheat your oven to 350 degrees F.

2. Fill the muffin tins with liners.

3. Whisk together gluten free flour, cinnamon, allspice, and baking soda in a medium mixing bowl.

4. Beat together butter and sugar until creamy and fluffy in a large bowl.

5. Add eggs, applesauce, and vanilla extract. Stir until smooth.

6. If you're using raisins (or another mix-in like chocolate chips or dried cranberries) place them in a small bowl. Add 2 tablespoons of the flour mixture and toss to coat.

This helps keep the mix-ins from sinking to the bottom of the muffin cups.

Gradually add dry to wet ingredients just until the muffin batter is just moistened. Don't over mix the batter!

7. Fold in raisins (or other mix-ins), if using.

8. Divide batter in the muffin pan using the cookie dough scoop.

9. Bake for 20-25 minutes until golden brown. Or until a toothpick inserted in the center comes out clean.

10. Cool muffins on a wire rack.

11. Serve room temperature or warm. Store leftovers in an airtight container.

A wire basket of applesauce muffins with a broken muffin in front and a bowl of fresh strawberries with a blue and white tea towel.

Equipment needed to make the applesauce muffins

  • (2-3) 6 cup or a 12 cup muffin pan

  • muffin liners, which are the same thing as cupcake liners or paper liners

  • cookie scoop

  • cake tester - I like this better than using a toothpick

  • wire rack

How to make muffins that are gluten free

For the best results, this simple gluten-free muffin recipe uses Bob's Red Mill Gluten-Free 1-to-1 Baking Flour. This is my favorite gluten free all-purpose flour.

This type of gluten-free flour blend has white rice flour, xanthan gum, potato starch, etc. so it bakes up just right and you don’t have to buy extra specialty ingredients.

How to measure flour

Don’t scoop the flour directly out of the bag with a measuring cup. It packs down the flour and you end up over measuring. Too much flour means your muffins may come out too dry.

Instead, spoon the flour from the bag (or the container you keep your flour in) into your measuring cup. Then use the back of a spatula or knife to level off the top of the cup.

That way the flour is given a mini-sift and isn't packed down.

Measure any type of flour this way – regular flour, oat flour, gluten free all-purpose flour, etc.

Check out my Best Gluten-Free Products List to find more terrific GF baking products!

Wire basket of applesauce muffins and glasses of milk on a white countertop.

What kind of applesauce?

You can use unsweetened applesauce from the store or homemade applesauce to make gluten free muffins.

If you only have sweetened applesauce on hand (or made sweetened homemade applesauce) cut back on the amount of sugar in the recipe.

You can also use cinnamon applesauce or pear applesauce.

No applesauce? Make pumpkin muffins or banana muffins by substituting 1 cup pumpkin purée or mashed banana for the applesauce.

Can I make these sugar-free gluten-free muffins?

YES! You can use no-calorie sweeteners like powdered monk fruit sweetener Swerve Sweetener in this gluten-free muffins recipe.

If you like the taste of brown sugar in your apple muffins you can use Swerve Sweetener, Brown. Both are terrific sugar-free substitutes.

What can I add to the muffins?

Toppings: Sprinkle cinnamon sugar or decorative sugar on the muffin tops. A sugar topping adds a fun crunch.

Mix-ins: Instead of raisins, you can use chopped nuts, dried cranberries, or chocolate chips in this gluten-free applesauce muffins recipe.

Fresh blueberries: I’d be a bit hesitant since fresh berries would add moisture to the muffin batter, which would affect baking time.

Instead, if you’re looking for a gluten-free blueberry muffin recipe, try my super popular Blueberry Muffin Cake, which is a cross between gluten-free blueberry muffins and coffee cake.

Muffins in a wire basket, two glasses of milk, a bowl of strawberries, and a blue and white napkin on a white countertop.

Can I make dairy-free or vegan muffins?

If you want to make dairy-free muffins or vegan muffins, here's what you need to do:

Butter: Use a vegan buttery spread like Earth Balance or coconut oil that's solid at room temperature. (Go for the buttery spread. It's tastier.)

Egg substitute: You can use Follow Your Heart egg substitute or Bob's Red Mill Gluten-Free Egg Replacer. You can also use flaxseed or aquafaba as an egg substitute.

Can I make mini muffins?

Yes, you can make mini gluten free applesauce muffins! You'll need a mini muffin pan, mini cupcake liners, and will have to adjust the baking time accordingly to about 10-12 minutes.

What's the best way to store these homemade muffins?

Store leftovers in an airtight container or Ziploc baggie in the fridge. They should stay good for up to a week.

Closeup of a broken muffin and a basket of applesauce muffins with a bowl of strawberries.

Can you freeze gluten free muffins?

I like making a big batch of muffins and freezing them for later. They make terrific weekday breakfasts or after-school snacks for the kids.

So the muffins don't stick together in a big frozen mass, you need to “flash” freeze them. Here's how:

1. Allow them to completely cool. Then place the muffins on a silicone mat or parchment-lined baking sheet. Then freeze them for 20 minutes.

2. Once the muffins are frozen, remove them from the baking sheet.

3. Then place them in a freezer-safe container or Ziploc freezer bag. (Remember to squeeze the air out of the bag to prevent freezer burn.)

4. Label and date the baggie or container. Store the muffins in the freezer for 3 to 4 months.

To thaw the frozen muffins, just place them on a plate for 30 minutes or so on the countertop.

You could also zap them on 50% power in the microwave, but I'd worry about drying them out.

If you want to heat the muffins, you can place them in the microwave for 10-15 seconds on high.

Are these healthy muffins?

I'm not a nutritionist, so I don't give advice or opinions.

However, you can add a few tablespoons of ground flaxseed to the muffin batter before baking. Since gluten free baking tends to lack whole grains, the flaxseed adds more fiber to your baking.

Raisins are a good source of fiber. Adding nuts to the recipe is an easy way to add some healthy fats and nutrition to this fluffy muffins recipe

A bowl of strawberries, a basket of freshly baked muffins, a glass of milk, and a napkin on a white tabletop.

More tips for making the best gluten-free applesauce muffins

Can I use coconut sugar instead of white sugar? Of course, you can also use coconut sugar instead of white sugar. Some people feel it’s healthier than white sugar.

Will my muffins stick to the pan? If you're concerned, you can use nonstick spray and then a paper liner. (This does help the liners stay put before you fill them.) But it's not necessary.

More gluten-free muffin recipes

These gluten-free muffin recipes are easy for first-time bakers:

Banana Oatmeal Muffins Recipe – these banana muffins are made with Cheerios

Zucchini Muffins Recipe – bake these with leftover zucchini from your garden

Healthy Strawberry Muffins Recipe – use your favorite strawberry yogurt

Raspberry Yogurt Muffins Recipe – one of my most popular recipes

Hash Brown Sausage Muffins Recipe – a savory muffin recipe that's perfect for breakfast

Yield: 12 to 18 MUFFINS

Gluten Free Applesauce Muffins Recipe

A wire basket of applesauce muffins with a broken muffin in front and a bowl of fresh strawberries with a blue and white tea towel.

This gluten-free muffin recipe makes a delicious breakfast or snack. These gluten-free applesauce muffins are easy to make in advance and freeze.

Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes


  • 2 cups all-purpose gluten free flour
  • 1 teaspoon ground cinnamon
  • 1 teaspoon ground allspice
  • 1 teaspoon baking soda
  • 1/2 cup (1 stick) unsalted butter, softened
  • 1 cup granulated sugar
  • 1 large egg, room temperature
  • 1 cup unsweetened applesauce
  • 2 teaspoons vanilla extract
  • 1/2 cup raisins, optional


  1. Preheat oven to 350 degrees F.
  2. Fill muffin tin with liners.
  3. In a medium bowl, whisk together flour, cinnamon, allspice, and baking soda.
  4. In a large mixing bowl, beat together butter and sugar until creamy and fluffy.
  5. Beat in eggs, applesauce, and vanilla until smooth.
  6. In a small bowl, add raisins and about 2 tablespoons of the flour mixture and toss to coat.
  7. Gradually add dry ingredients to wet ingredients just until the muffin batter is just moistened.
  8. Fold in raisins, if using.
  9. Divide batter into muffin tin using a cookie dough scoop.
  10. Bake for 20-25 minutes until golden brown or until a toothpick inserted in the center comes out clean.
  11. Cool muffins on a wire rack.
  12. Serve room temperature or warm.
  13. Store leftovers in an airtight container.

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Nutrition Information:



Serving Size:

1 muffin

Amount Per Serving: Calories: 121Total Fat: 1gSaturated Fat: 0gTrans Fat: 0gUnsaturated Fat: 0gCholesterol: 11mgSodium: 78mgCarbohydrates: 27gFiber: 1gSugar: 15gProtein: 2g

Nutritional information is automatically calculated per the ingredients list. Serving size may not be accurate. Please double-check with your preferred nutritional app for the most accurate information.

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