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Healthy Apple Crumb Muffins

These Healthy Apple Crumb Muffins are gluten-free and dairy-free and made with oat, quinoa, and almond flour. They're topped with a naturally-sweetened crisp streusel topping. The perfect fall treat!

If you have plans to go apple picking this fall, you're going to want to save this muffin recipe.

It's the perfect fall baking recipe to turn to when you have a fridge full of freshly picked fruit.

I love that these muffins are super moist and dense with a crisp crumb topping that's not overly sweet. These muffins are gluten-free and have a hearty texture and flavor from almond flour and almond butter.

If you love my Healthy Gluten-Free Apple Cake, you've got to try these muffins next!

ingredients for muffins with apples, sugar, eggs, vanilla and flour

How to Make Healthy Apple Crumb Muffins

This is a simple muffin recipe. You won't need any special equipment, just two mixing bowls, and a muffin tin.


Here's what you need to make gluten-free apple muffins:

  • Egg. This binds the batter together and provides structure.
  • Milk. You can use any milk you like, including a dairy-free option like almond milk.
  • Banana. Choose nice ripe bananas for the best flavor and texture.
  • Maple syrup. Honey will also work.
  • Apple cider vinegar. This adds acid to help the baking powder activate.
  • Oat flour. I like to use Bob's Red Mill.
  • Quinoa flour. This adds a nice nutty flavor to the muffins.
  • Almond flour. One of my favorite gluten-free flour options that adds healthy fats and heft to these muffins.
  • Coconut sugar. You can also use regular sugar if you prefer.
  • Baking powder and baking soda to lift and lighten the muffins.
  • Cinnamon. The must-have fall spice!
  • Apple. You can use any kind of apple you like. Granny Smith apples tend to hold their shape well during baking.

pouring white glaze over an apple crumb muffin

Crumble Topping

I like a crisp muffin top, but sometimes streusel can be so sweet and heavy it turns into dessert. The crumb topping on these apple muffins is lighter but adds the same crisp texture.

To make it, you'll use:

  • Oats. Use old-fashioned or rolled oats.
  • Quinoa flour. To help hold it together.
  • Almond flour. For more of that nutty flavor.
  • Oil. You can use coconut, avocado or another neutral oil.
  • Maple syrup. Honey works too!

bitten apple muffin with white glaze

Storing Leftovers

Store the muffins in an airtight container at room temperature for up to two days.

I like to zap them in the microwave for 10 seconds before serving them.

Can I Freeze Muffins?


Just let the muffins cool fully to room temperature first. Then pack them into an airtight container or bag and freeze them for up to 3 months.

You can defrost the muffins on the counter or reheat them in the microwave for 2-3 minutes to serve.

close up on baked apple crumb muffins

More Gluten Free Muffin Recipes

If you make these gluten-free Apple Crumb Muffins, be sure to let me know what you think with a comment below!

Healthy Apple Crumb Muffins

4.8 from 4 votes
These healthy Apple Crumb Muffins are gluten free and naturally sweetened for the perfect fall baking recipe.
author: Alyssa
yield: 12 muffins
pouring white glaze over an apple crumb muffin
Prep: 8 minutes
Cook: 22 minutes
Total: 30 minutes


For the muffins:

For the topping:


  • Heat the oven to 350ºF. Grease a 12-cup muffin tin and set aside.
  • In a small bowl, beat together the egg, banana, milk, sweetener, and vinegar.
    collage of two bowls with wet ingredients for apple muffins
  • Add the dry ingredients directly into the bowl with the wet and stir to thoroughly combine. Fold in the apple.
    collage of bowls with apple muffin batter
  • Quickly make the topping my mixing it all together in a bowl.
    collage of mixing ingredients for muffin crumb coating
  • Fill each cup 3/4 of the way full and top with about 1 tablespoon or so of crumble topping.
    overhead of a muffin tin filled with apple batter
  • Bake on the center rack for 22 - 24 minutes until a cake tester inserted into the center comes out clean.
  • Cool in the pan for 2 - 3 minutes, then transfer to a wire rack and cool completely. Resist the urge to not break into them; cooling them will allow everything to set properly.
    close up on baked apple crumb muffins
  • If desired, reheat in the toaster oven or in the microwave.


Storage Tips:

  • Room temperature: muffins can be stored in a sealed container at room temp for 2 days. Enjoy at room temp or heat in the microwave for 10 seconds.
  • Refrigerator: muffins can be stored in a sealed container in the fridge for up to 4 days. Heat in the microwave for 10 seconds before eating.
  • Freezer: wrap the muffins in foil, then store in a sealed container for up to 3 months. Reheat in the microwave for 20 seconds.


Serving: 1muffin | Calories: 233kcal | Carbohydrates: 34g | Protein: 6g | Fat: 9g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 14mg | Sodium: 188mg | Potassium: 228mg | Fiber: 4g | Sugar: 12g | Vitamin A: 37IU | Vitamin C: 2mg | Calcium: 99mg | Iron: 2mg
cuisine: American
course: Breakfast

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9 comments on “Healthy Apple Crumb Muffins”

  1. can a flax ‘egg” be used instead of the whole egg? Or can I use just egg whites; how many in place of a whole egg?
    Thank you.