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Apple Cinnamon Muffins

These Apple Cinnamon Muffins are spiced with cozy cinnamon and feature a moist, tender crumb, crisp streusel topping, and plenty of baked apples. They’re made with oat, quinoa, and almond flour, so they’re gluten-free and dairy-free too!

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

It's the perfect fall baking recipe to turn to when you have a fridge full of freshly picked fruit—and it’s much healthier than your average apple pie or crisp. 

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. Hello perfect breakfast!

If you love my Healthy Gluten-Free Apple Cake and other apple muffins like Apple Cider Muffins and Healthy Honey Applesauce Blender Muffins, you've got to try these apple cinnamon muffins next!

close up on baked apple cinnamon muffins

Why You’ll Love This Apple Cinnamon Muffin Recipe

Here’s what makes these apple cinnamon muffins extra special:

  • Muffins that are actually healthy. Let’s be real: those giant bakery-style muffins are loaded with sugar and oil, making them more of a decadent dessert than reasonable breakfast. These apple cinnamon muffins are totally breakfast-worthy, with no refined sugar or added oil.
  • Perfect texture and cozy flavor. The combination of flours—along with the banana—gives these apple cinnamon muffins a tender crumb, while the cinnamon and apples are everything we love about fall!
  • Easy to whip up. Like most muffin and quick bread recipes, this one comes together with minimal effort and prep time. Just mix everything together and bake!
Overhead view of ingredients for apple cinnamon muffins

What You’ll Need

Here are all of the ingredients you’ll need when making these healthy apple cinnamon muffins. Make sure to check out the recipe card at the bottom of the page to see the exact quantities for each ingredient. 

  • 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. Learn more: How to Use Quinoa Flour for Baking and Cooking
  • Almond flour – One of my favorite gluten-free flour options, which 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.

For the Crumble Topping:

  • 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!

How to Make Apple Cinnamon Muffins

It’s muffin time! Here’s what you’ll need to do to make this recipe.

  • Prepare. Preheat your oven to 350ºF and grease a 12-cup muffin pan.
Side-by-side photos of unmixed wet ingredients and mixed wet ingredients
  • Beat the wet ingredients. In a small mixing bowl, beat together the egg, banana, milk, sweetener, and vinegar.
Side-by-side photos of dry ingredients added to muffin batter and dry ingredients stirred into batter
  • Add the dry ingredients. Stir the dry ingredients into the bowl with the wet ingredients.
Side-by-side photos of apples added to muffin batter and apples stirred into muffin batter
  • Finish the batter. Gently fold the apples into the batter.
Side-by-side photos of unmixed crumb topping and mixed topping
  • Make the topping. Mix all of the topping ingredients in another bowl.
Side-by-side photos of apple cinnamon muffin batter in pan and batter topped with crumb mixture
  • Assemble. Fill each muffin cup 3/4 of the way full. Top with about 1 tablespoon of the crumble topping.
  • Bake. Place the pan in the oven and bake on the center rack for 22 to 24 minutes, or until a cake tester inserted into the center comes out clean.
  • Cool. Let the muffins cool in the pan for 2 to 3 minutes, then transfer them to a wire rack to finish cooling.

Tips for Success

Follow these additional pointers for perfect apple cinnamon muffins.

  • Use the best apples you can find. You can’t turn mealy, flavorless apples into delicious muffins! You want to use apples that taste good out of hand—if you’d want to eat them for a snack, you’ll want to eat them in muffins too.
  • Don’t switch up the flours. This recipe was developed with the specific flours listed here. Each brings different qualities to the table and if you switch one out with something else, it can affect how the recipe turns out. 
  • Be patient. Although warm apple cinnamon muffins are hard to resist, let them cool completely before serving them. They’ll hold together much better that way!


You can easily swap the apples for pears for a different spin on this recipe, or use a combination of the two fruits. Add chopped pecans or walnuts for crunch too if you’d like. 

Another option is to add a glaze over the top. My go-to is coconut butter—when it’s warmed up, you can drizzle it over the tops of the apple cinnamon muffins, then it turns solid when it cools. I also use it to glaze my pumpkin cookies.

pouring white glaze over an apple cinnamon muffin

How to Store

Store the apple cinnamon muffins in an airtight container at room temperature for up to 2 days.

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

Can I Freeze This Recipe?

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.

bitten apple cinnamon muffin with white glaze

More Gluten Free Muffin Recipes

Healthy Apple Cinnamon Muffins

4.8 from 4 votes
Apple cinnamon muffins are spiced with cozy cinnamon and feature a tender crumb, crisp streusel topping, and plenty of baked apples. So good!
author: Alyssa
yield: 12 muffins
pouring white glaze over an apple cinnamon 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 cinnamon 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 muffin 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 cinnamon 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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