Baked Goods & Desserts, Brunch It Up, Muffins

The Best Gluten-Free Apple Crumble Muffins Made Easy


Whether you’re looking for a sweet treat or tasty baked good for Sunday brunch, these gluten-free Apple Crumble Muffins are for you!

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An Apple a Day…

Growing up, my grandma and mom would make a homemade apple pie every Thanksgiving. As I got older and became more involved in the kitchen, I slowly learned the secrets to the infamous pie. My favorite part was always sautéing the apples in butter and spices to get them soft for the pie. And of course, eating a slice of the warm pie with a scoop of vanilla ice cream.

You can’t always wait all year for apple pie though. Plus, sometimes you don’t want the hassle of making a pie from scratch. Luckily, that’s where Apple Crumble Muffins come in! These gluten-free sweet treats have all of the delicious, warm flavors of traditional apple pie. They’re so much easier to make, yet are just as comforting as a slice of apple pie on Thanksgiving.

I love this gluten-free apple crumble muffin recipe because it’s the perfect baked good to enjoy no matter the time of day! Are you looking for a super quick breakfast? Muffins. A post lunch snack? Muffins. How about a post dinner dessert? More muffins. Whether you’re taking bites between your morning coffee or serving it up as an after school snack, you can’t go wrong with these gluten-free Apple Crumble Muffins!

Bite of an apple crumble muffin with bits of baked apple inside topped with a gluten-free crumble
Just look at that moist interior and crumbly topping!

Dairy-Free and Gluten-Free Apple Crumble Muffins

Like all of the recipes on my blog, these muffins are 100% gluten-free. But did I mention that they’re also dairy-free? These muffins use coconut oil in place of butter for a lighter and dairy-free alternative.

Coconut oil is a great alternative for many reasons. One being that it is in fact healthier than good ol’ butter. It contains a high percentage of MCTs (medium-chain triglycerides); which, is easier for the body to process and burn as energy than other types of fat. Also, coconut oil promotes hair and skin health! Talk about a win-win!

All in all, coconut oil serves as a great dairy-free alternative to butter in this apple crumble muffin recipe. It acts as a great bonding agent and maintains that infamous moist texture that makes muffins so scrumptious. Some other options may include:

  • Applesauce: This is a tasty alternative to butter or coconut oil. Just remember to opt for an unsweetened applesauce!
  • Coconut Yogurt: With a more solid texture, this alternative is great at providing a light consistency to baked goods. It also yields a creamy and tangy taste!
  • Bananas: As we know them to be a sweet treat, they will surly impart the same sweetness in your batter! Bananas are perfect for dense baked goods, as they provide a creamier consistency when incorporated.
  • Vegetable Oil: Did you know vegetable oil is essentially flavorless? This option is great at maintaining a moist texture while imparting no added flavor to the finished product.

Mashed banana or applesauce would also serve as a great match for this recipe in place of coconut oil. However, I craved a bit more lightness for this muffin’s texture. Therefore, I have found that coconut oil is the perfect substitution for butter in this case! If you want a muffin with a little more denseness, opt for one ripe, mashed banana or four tablespoons of applesauce.

The Best Baking Apple

First thing’s first, we need to talk about the kind of apple we are going to use for this recipe. There’s countless kinds of apples to choose from. So, how do you know which one is best?

  • Fuji: With a fresh and crisp texture and taste, this apple has a predominately sweet flavor making it a great option for any baked good as it holds its shape nicely under high heat.
  • Honeycrisp: This apple is the perfect balance of sweet and tart. With a mildly aromatic flavor, the honey crisp apple is the perfect choice for salads!
  • Granny Smith: Having a distinct citrusy/tart flavor with lime and grapefruit notes, this apple actually serves as a great baking apple as it balances out the sugar.
  • Golden Delicious: This apple is more mild, sweet, tangy and slightly aromatic in flavor. This one is great for pies, sauces, and preserves!

When it comes to this apple crumble muffin recipe though, the best kind of apple to use is Granny Smith Apples. Granny Smith apples are famous for their light green exterior and soft interior. I’m also sure we know them to be the “sour” apple as well. So, why the Granny Smith apple?

It may seem odd that Granny Smith apples are the best choice for this baked good when they have an inherently tart flavor. When baked, this citrusy flavor balances well with the sugar in the recipe. They also take on the delicious flavors they’re cooked with, like cinnamon. These apples also hold their form nicely when baked; which, makes them the perfect choice for this recipe!

Tray of apple crumble muffins.
How can you resist grabbing one of these muffins to enjoy on a nice fall day?

Seasoning and Cooking the Apples

Now that we know which apples are best for baking, let’s get started. Take two apples and carefully peel them before dicing into small cubes. Next, add the apples to a medium-sized bowl and season with brown sugar and spices. The spice blend brings out the natural sweetness of the apples using cinnamon, nutmeg, cloves and a pinch of salt. As well, they create that rich, warm flavor often associated with apple pies, fall, and holiday baking.

Next, add the coconut oil to a medium saucepan and melt over medium-high heat. After the coconut oil is melted, add your apples and sauté over medium-low heat for 10 minutes until golden and softened. It’s important to cook down the apples before adding them to the batter for a number of reasons.

  1. Cooking the apples releases the liquid from the fruit. Without this step, the apples would sink to the bottom of the muffin batter.
  2. Precooking the apples helps you to avoid crisp apples that haven’t softened enough.
  3. The apples are able to absorb more flavor as they’re sautéed in the brown sugar and spice blend.

Once the apples have cooked down and are slightly soft, allow them to cool completely. Adding hot or even warm apples to the batter can affect the overall consistency of the muffin. You want the apples to cool to room temperature for at least ten minutes.

sliced apple crumble muffin on a baking tray
These muffins pair perfectly with coffee for a sweet morning breakfast.

The Muffin Batter

Much like the rest of this recipe, this gluten-free batter is a breeze to make! Start by preheating the oven to 350 degrees and lining your muffin tin with silicone or paper liners. Then, sift your dry ingredients into a medium-sized bowl. Your dry ingredients will include: gluten-free flour, cinnamon, baking soda, salt, cloves, and nutmeg.

It is important to find a gluten-free flour that will still act like a regular flour without compromising texture. I have found that Bob’s Red Mill Gluten Free 1-to-1 Baking Flour acts and tastes the best for the majority of my gluten-free recipes! The cinnamon, salt, cloves and nutmeg serve an important role in creating the flavor profile of the muffin. These ingredients will give your muffins that class cinnamon-spice flavor! Don’t forget about the baking soda- this is crucial ingredient allows your muffins to rise. Otherwise, you might end up with flat, dense muffins.

Next, add one room temperature egg to a large mixing bowl with cane sugar and brown sugar. Use an electric mixer to beat the ingredients for one to two minutes on medium speed. Next, add the dairy-free yogurt. I like to use plain coconut yogurt as my dairy-free option, but the choice is yours. Then, add the melted coconut oil, almond milk and vanilla extract. Mix again until thoroughly combined.

Sift in the dry ingredients, half at a time and mix between. This help ensures that the ingredients are being dispersed evenly amongst the batter. Now for the fun part! Use a spatula to fold in the cooled apples into the batter. Finally, pour the batter into the silicone liners, filling about three fourths of the way before adding the crumble.

gluten-free apple crumble muffin
This muffin is just waiting to be devoured!

The Perfect Crumble

In a small bowl, we are going to add the dry ingredients for the crumble. This will include more gluten-free flour, cinnamon, and brown sugar. The flour will act as a base to marry all of the desired flavors together to create the perfect crumble. We want the crumble to be packed with rich cinnamon and the sweetness from the brown sugar. Once all three ingredients are mixed, we will slowly add in the melted coconut oil. The coconut oil will give the dry ingredients the “crumble” texture, allowing them to combine and create this beautiful topping for our muffins. After you have mixed all ingredients together with a whisk or fork, set aside.

Now it’s time to add the crumble to the top of the muffin batter! Add one spoonful of the crumble to the top of each muffin. Once the crumble is added and the oven is preheated, place the muffin tin on the center rack. Bake for 25 minutes and broil on low for three to five minutes. Keep a close eye on the muffins when broiling, as the crumble can quickly burn. Then, remove from the oven and allow to cool in the liners for 15 minutes before carefully removing.

An apple crumble muffin sitting on a baking sheet after cooling from the oven. A top view of the muffin to enhance the look of the crumble on top.

How to Store These Gluten-Free Apple Crumble Muffins

It’s important to allow the apple crumble muffins to cool to room temperatures. Not only does this allow the flavors to fully mature, but it’s also best for storage purposes. While it’s best to eat these muffins fresh, you’ll probably end up storing a good bit of the batch. Once cooled to room temperature, store in a cover container outside of the refrigerator. The muffins can be stored up to four days, but I doubt they’ll last that long!

Apple Crumble Muffins

Recipe by Arianna LitrentaCourse: Muffins, BrunchDifficulty: Easy


Prep time


Cooking time



Whether you’re looking for a sweet treat or tasty baked good for Sunday brunch, these Apple Crumble Muffins are for you!


  • For the Apples
  • 2 cups of Granny Smith apples, peeled and thinly diced

  • 2 tablespoons brown sugar

  • 1 tablespoon cinnamon

  • ¼ teaspoon nutmeg

  • ¼ teaspoon cloves

  • Pinch of salt

  • 2 teaspoons coconut oil

  • For the Crumble
  • 1 cup of gluten-free baking flour

  • 1 cup brown sugar

  • 1 tablespoon cinnamon

  • 5 tablespoons coconut oil, melted

  • For the Batter
  • 2 cups gluten-free baking flour

  • 1 teaspoon cinnamon

  • ¾ teaspoon baking soda

  • ¼ teaspoon salt

  • ¼ teaspoon cloves

  • ¼ teaspoon nutmeg

  • 1 cup cane sugar

  • 1 tablespoon brown sugar

  • 1 egg, room temperature

  • ¾ cup coconut yogurt, dairy-free

  • ½ cup coconut oil, melted

  • 2 tablespoons almond milk

  • 1 teaspoon vanilla extract


  • For the Apples
  • Peel and dice the apples, then toss with the brown sugar and spice blend.
  • Add the coconut oil to a large pan, then turn the heat to medium
  • Once melted, add your apple mixture
  • Cook over medium heat for 10 minutes, then allow to cool for 10 minutes
  • For the Crumble
  • Add the dry ingredients to a small bowl, then add the coconut oil
  • Mix together with a whisk, then set to the side
  • For the Batter
  • Preheat the oven to 350 degrees Fahrenheit and line a muffin tin with silicone liners
  • Add the dry ingredients to a medium-sized mixing bowl
  • Next, in a large bowl, combine the eggs and sugars
  • Beat with an electric mixer for 1 minute, then add the wet ingredients
  • Combine and beat for another minute before slowly adding the dry ingredients 
  • Beat again for 1 minute, then use a spatula to fold in the apples 
  • Add the batter to the liners, filling ¾ of the way 
  • Lightly sprinkle the top of each muffin with a spoonful of the crumble
  • Bake for 25 minutes, then broil on high for 2 minutes to get the crumble golden
  • Allow to cool for 10 minutes before serving 

Recipe Video


  • Store these muffins in an air tight container up to four days.

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