15 Gluten Free Fall Muffins

ByNabeela Dastagir

Muffins are one of the easiest ways to enjoy fall’s best flavors in a portable, grab-and-go form, and these 15 gluten free fall muffins prove you don’t need wheat flour to get soft, moist results.

Made with gluten free flour blends, almond flour, and seasonal ingredients like pumpkin, apple, and cranberry, these muffins are perfect for breakfast, snacking, or an afternoon treat.

Whether you love classic pumpkin spice or something a little different like chai spice or pear ginger, there’s a recipe here for every fall craving.

Let’s bake up 15 warm, gluten free muffins to fill your kitchen with cozy autumn scents.

1. Pumpkin Spice Muffins

Soft, moist muffins bursting with pumpkin flavor and warm fall spices. These classic gluten free muffins are a must-bake every autumn.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 cup pumpkin puree
  • 2 eggs
  • 1/2 cup brown sugar
  • 1/3 cup melted coconut oil
  • 1 tsp baking soda
  • 2 tsp pumpkin pie spice

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, baking soda, and pumpkin pie spice.
  3. In another bowl, mix pumpkin puree, eggs, brown sugar, and coconut oil.
  4. Combine wet and dry ingredients until just mixed.
  5. Divide batter into muffin cups and bake 20-22 minutes until a toothpick comes out clean.

Nutritional Facts (per serving): Calories: 210 | Protein: 4g | Carbs: 28g | Fat: 9g

2. Apple Cinnamon Almond Flour Muffins

Moist, tender muffins made with almond flour and studded with diced apple. These naturally gluten free muffins have a rich, nutty flavor.

Ingredients:

  • 2 cups almond flour
  • 1 apple, finely diced
  • 3 eggs
  • 1/3 cup maple syrup
  • 1 tsp baking soda
  • 1 tsp cinnamon

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together almond flour, baking soda, and cinnamon.
  3. In another bowl, mix eggs and maple syrup.
  4. Combine wet and dry ingredients, then fold in diced apple.
  5. Divide batter into muffin cups and bake 20-25 minutes until golden.

Nutritional Facts (per serving): Calories: 220 | Protein: 8g | Carbs: 14g | Fat: 16g

3. Banana Nut Muffins

Classic banana muffins loaded with chopped walnuts, made with a gluten free flour blend. They’re moist, naturally sweet, and perfect for using up ripe bananas.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 3 ripe bananas, mashed
  • 2 eggs
  • 1/3 cup melted butter
  • 1/2 cup brown sugar
  • 1 tsp baking soda
  • 1/2 cup chopped walnuts

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour and baking soda.
  3. In another bowl, mix mashed bananas, eggs, melted butter, and brown sugar.
  4. Combine wet and dry ingredients, then fold in walnuts.
  5. Divide batter into muffin cups and bake 20-22 minutes until a toothpick comes out clean.

Nutritional Facts (per serving): Calories: 230 | Protein: 5g | Carbs: 30g | Fat: 11g

4. Sweet Potato Muffins

Soft, subtly sweet muffins made with mashed sweet potato and warm spices. These gluten free muffins are a great way to use up leftover sweet potato.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 cup mashed sweet potato
  • 2 eggs
  • 1/3 cup melted coconut oil
  • 1/2 cup brown sugar
  • 1 tsp baking soda
  • 1 tsp cinnamon

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, baking soda, and cinnamon.
  3. In another bowl, mix mashed sweet potato, eggs, coconut oil, and brown sugar.
  4. Combine wet and dry ingredients until just mixed.
  5. Divide batter into muffin cups and bake 20-22 minutes until set.

Nutritional Facts (per serving): Calories: 200 | Protein: 4g | Carbs: 27g | Fat: 8g

5. Cranberry Orange Muffins

Bright, tangy muffins studded with fresh cranberries and a hint of orange zest. These gluten free muffins are festive and full of fall flavor.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 cup fresh cranberries, chopped
  • 2 eggs
  • 1/3 cup melted butter
  • 1/2 cup sugar
  • Zest of 1 orange
  • 1 tsp baking powder

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour and baking powder.
  3. In another bowl, mix eggs, melted butter, sugar, and orange zest.
  4. Combine wet and dry ingredients, then fold in chopped cranberries.
  5. Divide batter into muffin cups and bake 20-22 minutes until golden.

Nutritional Facts (per serving): Calories: 210 | Protein: 4g | Carbs: 29g | Fat: 9g

6. Carrot Cake Muffins

Moist, spiced muffins packed with shredded carrots and topped with a light cream cheese glaze. These gluten free muffins taste just like carrot cake.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 1/2 cups shredded carrots
  • 2 eggs
  • 1/3 cup melted coconut oil
  • 1/2 cup brown sugar
  • 1 tsp cinnamon
  • 1 tsp baking soda

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, cinnamon, and baking soda.
  3. In another bowl, mix eggs, coconut oil, and brown sugar.
  4. Combine wet and dry ingredients, then fold in shredded carrots.
  5. Divide batter into muffin cups and bake 20-22 minutes until a toothpick comes out clean.

Nutritional Facts (per serving): Calories: 220 | Protein: 4g | Carbs: 30g | Fat: 9g

7. Maple Pecan Muffins

Rich, nutty muffins sweetened with maple syrup and topped with crunchy pecans. These gluten free muffins are perfect with a warm cup of coffee.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 2 eggs
  • 1/2 cup maple syrup
  • 1/3 cup melted butter
  • 1 tsp baking powder
  • 1/2 cup chopped pecans

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour and baking powder.
  3. In another bowl, mix eggs, maple syrup, and melted butter.
  4. Combine wet and dry ingredients, then fold in chopped pecans.
  5. Divide batter into muffin cups and bake 18-20 minutes until golden.

Nutritional Facts (per serving): Calories: 220 | Protein: 4g | Carbs: 28g | Fat: 11g

8. Pumpkin Chocolate Chip Muffins

Soft pumpkin muffins studded with melty chocolate chips. These gluten free muffins are a sweet treat that still feels like a fall classic.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 cup pumpkin puree
  • 2 eggs
  • 1/3 cup melted coconut oil
  • 1/2 cup brown sugar
  • 1 tsp pumpkin pie spice
  • 1/2 cup chocolate chips

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour and pumpkin pie spice.
  3. In another bowl, mix pumpkin puree, eggs, coconut oil, and brown sugar.
  4. Combine wet and dry ingredients, then fold in chocolate chips.
  5. Divide batter into muffin cups and bake 20-22 minutes until set.

Nutritional Facts (per serving): Calories: 240 | Protein: 4g | Carbs: 32g | Fat: 11g

9. Zucchini Bread Muffins

Moist, lightly spiced muffins made with shredded zucchini. These gluten free muffins are a great way to sneak in extra vegetables.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 1/2 cups shredded zucchini
  • 2 eggs
  • 1/3 cup melted coconut oil
  • 1/2 cup brown sugar
  • 1 tsp cinnamon
  • 1 tsp baking soda

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, cinnamon, and baking soda.
  3. In another bowl, mix eggs, coconut oil, and brown sugar.
  4. Combine wet and dry ingredients, then fold in shredded zucchini.
  5. Divide batter into muffin cups and bake 20-22 minutes until golden.

Nutritional Facts (per serving): Calories: 200 | Protein: 4g | Carbs: 27g | Fat: 8g

10. Apple Crumb Muffins

Soft apple muffins topped with a crunchy cinnamon crumb topping. These gluten free muffins have the perfect balance of soft and crispy textures.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 apple, finely diced
  • 2 eggs
  • 1/2 cup brown sugar
  • 1/3 cup melted butter
  • 1 tsp cinnamon
  • 1/3 cup gluten free oats for topping

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, brown sugar, and cinnamon, then mix in eggs and melted butter.
  3. Fold in diced apple.
  4. Divide batter into muffin cups and sprinkle oats on top.
  5. Bake 20-22 minutes until golden.

Nutritional Facts (per serving): Calories: 220 | Protein: 4g | Carbs: 30g | Fat: 9g

11. Chai Spice Muffins

Fragrant muffins infused with warm chai spices like cardamom, cinnamon, and ginger. These gluten free muffins are cozy and aromatic, perfect for fall mornings.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 2 eggs
  • 1/2 cup brown sugar
  • 1/3 cup melted butter
  • 3/4 cup milk
  • 1 tsp cinnamon
  • 1/2 tsp cardamom
  • 1/2 tsp ground ginger

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, cinnamon, cardamom, and ginger.
  3. In another bowl, mix eggs, brown sugar, melted butter, and milk.
  4. Combine wet and dry ingredients until just mixed.
  5. Divide batter into muffin cups and bake 18-20 minutes until golden.

Nutritional Facts (per serving): Calories: 210 | Protein: 4g | Carbs: 29g | Fat: 9g

12. Pear Ginger Muffins

Soft muffins studded with diced pear and a hint of fresh ginger. These gluten free muffins offer a lighter, slightly floral take on fall baking.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 pear, finely diced
  • 2 eggs
  • 1/3 cup melted butter
  • 1/2 cup brown sugar
  • 1 tsp ground ginger
  • 1 tsp baking powder

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, ground ginger, and baking powder.
  3. In another bowl, mix eggs, melted butter, and brown sugar.
  4. Combine wet and dry ingredients, then fold in diced pear.
  5. Divide batter into muffin cups and bake 20-22 minutes until golden.

Nutritional Facts (per serving): Calories: 210 | Protein: 4g | Carbs: 29g | Fat: 8g

13. Butternut Squash Muffins

Moist muffins made with pureed butternut squash and warm spices. These gluten free muffins are a great alternative to pumpkin for fall baking.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 1 cup butternut squash puree
  • 2 eggs
  • 1/3 cup melted coconut oil
  • 1/2 cup brown sugar
  • 1 tsp cinnamon
  • 1 tsp baking soda

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, cinnamon, and baking soda.
  3. In another bowl, mix butternut squash puree, eggs, coconut oil, and brown sugar.
  4. Combine wet and dry ingredients until just mixed.
  5. Divide batter into muffin cups and bake 20-22 minutes until set.

Nutritional Facts (per serving): Calories: 210 | Protein: 4g | Carbs: 28g | Fat: 9g

14. Cinnamon Streusel Muffins

Soft vanilla muffins topped with a buttery cinnamon streusel crumb. These gluten free muffins are a sweet, comforting treat any time of day.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 2 eggs
  • 1/2 cup sugar
  • 1/3 cup melted butter
  • 3/4 cup milk
  • 1 tsp vanilla extract
  • 1/3 cup gluten free flour, 2 tbsp butter, and 1 tsp cinnamon for streusel topping

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour, eggs, sugar, melted butter, milk, and vanilla until smooth.
  3. Divide batter into muffin cups.
  4. Mix streusel ingredients together until crumbly, then sprinkle over the batter.
  5. Bake 18-20 minutes until golden.

Nutritional Facts (per serving): Calories: 230 | Protein: 4g | Carbs: 30g | Fat: 11g

15. Maple Walnut Muffins

Rich, nutty muffins sweetened naturally with maple syrup and studded with walnuts. These gluten free muffins are hearty and satisfying for a fall breakfast.

Ingredients:

  • 1 3/4 cups gluten free all-purpose flour blend
  • 2 eggs
  • 1/2 cup maple syrup
  • 1/3 cup melted butter
  • 3/4 cup milk
  • 1 tsp baking powder
  • 1/2 cup chopped walnuts

Instructions:

  1. Preheat oven to 350°F and line a muffin tin with liners.
  2. Whisk together flour and baking powder.
  3. In another bowl, mix eggs, maple syrup, melted butter, and milk.
  4. Combine wet and dry ingredients, then fold in chopped walnuts.
  5. Divide batter into muffin cups and bake 18-20 minutes until golden.

Nutritional Facts (per serving): Calories: 230 | Protein: 5g | Carbs: 29g | Fat: 11g

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