These Gluten-Free Apple Muffins are a quick and easy snack that your kids will love. They’re simple to make, and perfect for packing in a lunchbox or taking on the go. Plus, they’re loaded with healthy ingredients like cinnamon and apples, so you can feel good about eating them. 

Two gluten free apple muffins stacked on a counter.

Muffins are one of the best snack foods there is.

When you make your own you can control the amount of sugar and all the other ingredients, making them a healthy alternative to store-bought snacks.

I also love that muffins freeze and thaw well, so they are ready at a moment’s notice.

Why You Need This Recipe

  • Apples are wonderful when in season, and these muffins are a great way to preserve the bounty of the harvest.
  • The diced apples add a wonderful textural element. These healthy apple muffins make a great afternoon snack or perfect fall breakfast.
  • Customize your spices based on what you have on hand to make these your own.

Key Ingredients

Ingredients to make gluten-free apple muffins on a white surface.

Apples add fiber and create a wonderful texture when mixed into the batter. You can use any type of fresh apples including Honeycrisp apples, Fuji apples, Pink Lady apples, Gala apples, or your favorite variety.

Coconut oil or olive oil adds moisture and can create different tastes based on what you reach for. Use melted butter if you aren’t on a dairy-free diet.

Gluten-free flour is tested to work cup-for-cup in place of all-purpose flour for the best baking experience. I recommend Bob’s Red Mill Gluten-Free Baking Flour.

Select the milk of your choice to bring the batter together. To make these muffins both gluten-free and dairy-free, use a plant milk like almond milk.

Please see the recipe card at the end of this post for the exact ingredients and measurements.

Recipe Steps

Photo collage showing how to mix and bake gluten free apple muffins.

Step One

Preheat the oven and either oil or line with papers a muffin tin. Combine milk and lemon juice to rest in a small bowl.

Please see the recipe card at the end of this post for the exact ingredients and measurements.

Step Two

In a large mixing bowl, combine all dry ingredients and the diced apple. Add remaining wet ingredients to the flour mixture and stir to mix well.

Step Three

Divide muffin batter evenly into prepared muffin cups and bake until the toothpick test is clean.

Step Four

Let cool on a cooling rack and serve warm or at room temperature.

I hope your family loves these delicious and tender muffins as much as mine does! They are such a yummy treat during apple season.

A halved apple muffin stacked on a whole muffin.

Recipe Tips & Substitutions

  • You can use any type of red or green apple in this recipe.
  • Store any cooked muffins in an airtight container at room temperature for 2 days or in the refrigerator for up to 4 days.
  • You can also freeze any leftover cooked muffins in a ziptop bag for up to 2 months.
  • You may also like these Lemon muffins! Or, if you want a decadent treat, try this Apple Crumble Tart.

Recipe FAQs

Are these muffins vegan?

These muffins are gluten-free and dairy-free as written, but do contain an egg. I haven’t tested it, but you could try your favorite egg substitute such as chia or flaxseeds, and this recipe would then be vegan.

How do I freeze muffins?

Let them cool completely on a wire rack. At that point, you can place them in a freezer bag or an airtight container for up to 2 months. Let them thaw overnight to enjoy for breakfast.

Can I grate the apples?

Yes, you can grate the apples as opposed to chopping them if you prefer that textured over chopped apples.

Gluten free apple muffins on a wire rack.

More Healthy Muffin Recipes You Might Like

Don’t Miss These Apple Recipes!

Crockpot Applesauce Recipe Without Added Sugar

Instant Pot Apple Butter (No Added Sugar)

Air Fryer Apple Crisp (Gluten-Free & Vegan)

Healthy Instant Pot Baked Apples (5-Ingredients)

I hope you make this recipe! If you do, please leave a comment and a starred review below.

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Gluten free apple muffins on a wire rack.

Gluten-Free Apple Muffins

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5 from 2 reviews

Print Recipe

These Gluten-Free Apple Muffins are a quick and easy snack that your kids will love. They’re simple to make, and perfect for packing in a lunchbox or taking on the go. Plus, they’re loaded with healthy ingredients like cinnamon and apples, so you can feel good about eating them. 

  • Total Time: 45 minutes
  • Yield: 12 muffins

Ingredients

Units Scale
  • Nonstick cooking spray
  • 1 cup unsweetened almond milk (you can use regular milk if you are not on a dairy-free diet)
  • 1 tablespoon lemon juice
  • 2 cups gluten-free baking flour (I used Bob’s 1-to-1 Gluten-Free Baking Flour)
  • 1 apple, chopped into very small pieces
  • 2/3 cup sugar
  • 1 teaspoon ground cinnamon
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/3 cup olive oil or melted coconut oil
  • 1 egg, lightly beaten

Instructions

  1. Preheat your oven to 375°F. Spray a muffin tin lightly with nonstick cooking spray and set aside.
  2. In a small pitcher or bowl, combine the milk and lemon juice. Stir to combine and set aside.
  3. Then, in a large mixing bowl, combine the flour, apple, sugar, cinnamon, baking powder, baking soda, and sea salt. Stir to combine.
  4. Stir in the almond milk mixture, oil, and egg.
  5. Then, divide the batter between the muffin wells.
  6. Bake for 25 minutes, or until the muffins are cooked through and a toothpick or fork inserted into the center of one comes out clean. 
  7. Let the muffins cool for a few minutes in the tin. Then, remove them and serve warm or at room temperature.

Equipment

Notes

  1. You can use any type of red or green apple in this recipe.
  2. Store any cooked muffins in an airtight container at room temperature for 2 days or in the refrigerator for up to 4 days. You can also freeze any leftover cooked muffins in a ziptop bag for up to 2 months.

Nutrition

  • Serving Size: 1 muffins
  • Calories: 194
  • Sugar: 11.7 g
  • Sodium: 69.7 mg
  • Fat: 6.6 g
  • Saturated Fat: 0.9 g
  • Carbohydrates: 33.3 g
  • Fiber: 1.3 g
  • Protein: 1.6 g
  • Cholesterol: 0 mg

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About the Author: Carrie Forrest has a master’s degree in public health with a specialty in nutrition and is a certified holistic nutritionist. She is a top wellness and food blogger with over 5 million annual visitors to her site. Carrie has an incredible story of recovery from chronic illness and is passionate about helping other women transform their health. Send her a message through her contact form.