My husband adores apple muffins and this time of year, Apple Pumpkin Gluten Free Muffins are his favorite. These yummy muffins are filled with spicy goodness, sweet apples and luscious pumpkin puree, perfect for a crisp fall day, a cup of hot coffee and the ones you love sharing all the wonderful flavors of fall in every bite! And best of all, they’re gluten free!
I’ve been experimenting lately with different combos of gluten-free flours to come up with a baking mix that works well for muffins and quick breads and I’m eager to share my newest discoveries with you.
My suggestion is to make up a batch of this baking mix for anytime the desire hits to make homemade muffins or quick breads. This recipe makes 6 cups of gluten free baking mix.
Here’s my whole grain gluten-free baking mix:
- 2 cups Sorghum Flour
- 2 cups Gluten Free Whole Grain Oat Flour
- 1 1/3 cup Tapioca Flour
- 2/3 cup Pure Organic Corn Starch
Mix all the flours together thoroughly in a big bowl then store in a tupperware or glass jar. Just remember to mark it as gluten free. You can double this batch if you’d like to have a big stash. Whenever the mood strikes, use this mix in any recipe for whole grain muffins or quick breads. This works great for banana or pumpkin bread and pretty much any kind of muffin. You can find all these flours at your grocery store, Whole Foods or Amazon.
Another blend I’ve used successfully with this recipe is this one:
- 1 cup Honeyville Blanched Almond Flour Super Fine Grind (Honeyville is the only almond flour I use)
- ¼ cup Nutiva Organic Coconut Flour
- ¼ cup Bob’s Red Mill Tapioca Flour
- ¼ cup Bob’s Red Mill Organic Brown Rice Flour
When using the above blend I use 1 ¼ cups organic sugar instead of the coconut sugar. It seems to make them taste a bit lighter. I cooked the muffins a little longer with this blend, around 40 minutes at 350.
Apple Pumpkin Gluten Free Muffins
Makes 12
- 2½ cups gluten-free baking mix
- 1¼ cups coconut sugar (you can use brown sugar but coconut sugar is more nutrient dense and has a naturally lower glycemic index)
- ¾ teaspoon sea salt
- 1 teaspoon ground cinnamon
- 2 teaspoons pumpkin pie spice
- ½ cup melted butter or coconut oil
- 3 large, organic eggs
- 1 cup organic pumpkin puree,(not pumpkin pie mix)
- 2 cups cored and chopped organic apples
- 1 teaspoon pure vanilla extract
- Preheat oven to 350 and line a muffin pan with cupcake liners.
- Mix all the dry ingredients together in a bowl. Mix well.
- In a separate bowl, beat 3 eggs. Add pumpkin puree and vanilla and mix well.
- Add the melted butter or coconut oil slowly if it's hot as you don't want to cook the eggs. Add in a thin stream, whisking as you add.
- Now, add the wet mixture to the dry and blend thoroughly but gently, basically just to moisten.
- Stir in the chopped apples.
- Spoon batter into prepared muffin tins (I use an ice cream scoop) and smooth the tops.
- Sprinkle the streusel mix evenly across the muffin tops.
- Bake for 20-25 minutes until a cake tester comes out clean.
- Let cool 5 minutes. Remove hot muffins to a wire rack to cool.
- Serve with butter, cream cheese or apple butter.
- Streusel Topping: ¼ cup organic sugar, ¼ cup coconut flour, 1 ½ tablespoons butter, 1 teaspoon cinnamon, ¼ cup chopped pecans. Mix all ingredients together and sprinkle on top of muffins.

Kate’s Tips
- I always add ¼ cup of chopped pecans or walnuts to either the batter or the streusel topping. Feel free to exclude them if you don’t like nuts.
- You can substitute apple sauce for the pumpkin puree.
- Another fun addition would be chopped crystallized ginger or golden raisins.
- These muffins freeze well. Wrap each individually in plastic wrap and freeze in a plastic bag.
I’d love to know if you make them and how they turn out!

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