Gluten Free Apple Oatmeal Muffins

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Made with gluten free rolled oats, crisp apples, and warm spices, these Apple Oatmeal Muffins are gluten free, refined sugar free, and kid-friendly. Make them ahead of time for allergy-friendly breakfasts, lunchbox snacks, and more! Vegan option. 

3 gluten free apple oatmeal muffins stacked on top of each other

An Apple Muffin a Day Keeps the Doctor Away

It’s apple season, ya’ll, and did you know that the average American citizen eats about 20 pounds of apples each year? Yep, you read that right! Crazy, right? Although with recipes like Apple Cider Caramel Baked Apples, Almond Flour Apple Coffee Cake, and Creamy Apple Salad Wraps, I can see why. They’re just so dang delicious! Plus, this time of year, they’re super sweet and extra juicy making them perfect for baking. 

Not wanting the season to go to waste, I gathered a big bunch and jumped in the kitchen to whip up these apple oatmeal muffins! After all, who doesn’t love a good muffin recipe? Am I right? Whether you’re looking for an on-the breakfast, an afterschool snack, or even a nutritious dessert, they’re perfect for every occasion!

Of course, you could always buy pre-packaged varieties. However, they’re often filled with added sugar and not-so allergy-friendly ingredients. So, in an effort to create a packable muffin that can be enjoyed by everyone, I decided to create my own using gluten free whole grains, fresh fruit, and healthy fats for a snack perfect to take to school, the office, and wherever else the day might take you! Did I mention they’re super easy to make, too? I’ll prove it! 

three apple oatmeal muffins on a counter with a bite taken out of one

The Best Ingredients for Apple Oatmeal Muffins 

Gluten Free Rolled Oats – If you have it on hand, you can skip using rolled oats, and replace them with oat flour instead. You’ll probably want to keep some gluten free rolled oats on hand for the crumble topping, though! 

Pro Tip

Pro-Tip: Depending on the cut, different types of oat flour can weigh more or less. For accuracy, make sure the oat flour weighs the same as the grams listed in the recipe. Also, make sure you’re using certified gluten free oat flour, like Bob’s Redmill

Flax Meal – I like flax meal for the slightly nutty flavor it adds, but if you don’t have them available, you can replace them with chia seeds. Just make sure to grind them first!

Applesauce – Make sure you use unsweetened applesauce! Otherwise, your muffins might be too sweet for your liking. 

Non-Dairy Milk – Any non-dairy you like best works well for this recipe as long as it is not flavored. 

Nutrition Tip

Tip for Vegan Baking: Wanna know the secret to making these oat muffins vegan without sacrificing taste or texture? It’s all in how you combine a few special ingredients! Flax meal, applesauce, non-dairy milk, and apple cider vinegar come together to create a moist texture and plenty of fluff without the need for eggs or gluten! Not to mention, they add lots of nutrients and fiber!

Maple Syrup – For the richest flavor, I highly recommend using real maple syrup if you’ve got it. However, honey can be used as well. Just make sure it’s the same viscosity as the maple syrup. Not too thick! 

ingredients for gluten free apple oatmeal muffins on a counter

Apple Cider Vinegar – The secret ingredient in these apple muffins, apple cider vinegar helps them rise to create that light, fluffy texture we all love, but lemon juice works, too! 

Apples – Technically, apples are optional, but they are highly recommended! For the sweetest flavor, use red apples such as Jonagold, Honeycrisp, or Pink Lady. 

Nutrition Tip

Nutrition Tip: Did you know a medium-sized apple provides 17% of the daily recommended amount of fiber? Not to mention, it’s full of vitamins and minerals such as vitamin C and potassium!  

How to Make Flourless Muffins with Oats

Unlike other muffin recipes that can be super elaborate and use every dish in the kitchen, these muffins are quick and easy! All you’ll need is a couple of bowls and a muffin tin, and you’ll be filling your home with warm apple cinnamon scents. 

Mix. In a large bowl, mix together all of the dry ingredients. Or, just toss them in a blender and give them a few pulses to combine. If you used whole oats, you’ll have the blender out to make oat flour, anyway! 

Pro Tip

Note: Oat flour (if grounding your own oats) tends to clump together. So, be extra careful to remove any flour clumps when stirring. 

Whisk. In a separate smaller bowl, whisk together all of the wet ingredients until they are evenly combined. 

Combine. Gently add the wet batter to the dry batter, and stir in the apple cider vinegar. 

Pro Tip

Pro-Tip: Don’t overmix your batter, or the muffins won’t rise! Think of it like a pancake mix, and stir the ingredients until they are just combined and all the clumps are removed. 

Spoon. Add the batter to lined muffins pans, filling them about ⅔ of the way full. 

Pro Tip

Note: For added texture and flavor, gently fold chopped apples (peeled or with skin) into the batter before adding them to the muffin tins. 

Top. Combine rolled oats, chopped apples, and coconut sugar in a small bowl, and sprinkle the mixture on top of the muffins. 

Bake. Place the muffin tins in the oven for 18-22 minutes or until a toothpick can be inserted and comes out clean. Once they have finished baking, be sure to let the muffins cool on a cooling rack for 5-10 minutes before eating. Otherwise, they might fall apart! 

muffin tin with gluten free apple oatmeal muffin being held wtih 2 hands

Extra Apple Muffins Add-Ins

This recipe has tons of great texture and flavor on its own, especially if you add the chopped apples to the center. However, we all like options, right? So, if you want to switch things up try including chopped nuts, dark chocolate chips, or even unsweetened coconut shreds.

Gluten free apple oatmeal muffin being held with a bite taken out
SHYANNE this is extra so might not need to use

Storage Tips

To keep your muffins super soft and moist, store them in an airtight container in the fridge, but first, place a layer of paper towels in the bottom of the container. Then, add the muffins in a single layer, and top them with another paper towel. This will help keep the moisture in, and your apple oatmeal muffins will stay fresh for up to 4 days. 

Can I Freeze Flourless Muffins? 

Yes! In fact, I recommend doing so for quick breakfasts and easy snacks. Just place your muffins in a sealable bag, and store them in the freezer for up to 3 months. 

Pro Tip

Pro-Tip: To reheat frozen muffins, place them in the fridge to thaw. Then, pop them in the oven at 350 degrees for a few minutes or until they are heated through.

gluten free apple oatmeal muffins on a cooling rack in a muffin liner


gluten free applesauce muffin with oat topping

Flourless Apple Oatmeal Muffins (Vegan)

  • Author:
    Lindsay Cotter

  • Prep Time:
    10 minutes

  • Cook Time:
    18-22 minutes

  • Total Time:
    28-32 minutes

  • Yield:
    9-11 muffins

  • Diet:
    Gluten Free


These kid-friendly Gluten Free Apple Oatmeal Muffins are made with rolled oats and natural sugars for a healthy breakfast or quick snack that can be prepared ahead of time! Vegan friendly. 



  • 2 cups (160 grams)* gluten free rolled oats plus extra for topping. Gluten free oat flour may be substituted. (Equals about 1 1/2 cups oat flour)
  • 2 Tablespoon flax meal
  • 1/4 teaspoon of salt
  • 1 1/2 teaspoon baking powder
  • 1 1/2 teaspoon baking soda
  • 2 teaspoon ground cinnamon
  • 1/4 teaspoon ground ginger
  • 1/4 teaspoon ground nutmeg
  • 3/4 cup unsweetened applesauce
  • 2/3 cup non dairy milk
  • 1/3 cup maple syrup
  • 2 teaspoon apple cider vinegar or lemon juice
  • Optional – 1/2 cup diced or shredded apple (peeled) to fold into batter + extra for topping
  • Topping – 1/3 diced apple, 1/4 c rolled oats, coconut sugar substitute such as brown sugar swerve


  1. Preheat oven to 350. Line or grease a muffin tin; set aside.
  2. In a large bowl, mix dry ingredients together, making sure to remove any flour clumps. (Alternatively, place these ingredients in a blender and blend until combined. If using rolled oats, versus oat flour, use a blender to grind the oats into a fine flour first.)
  3. Whisk the applesauce, milk, and maple syrup together in a medium bowl until combined.
  4. Combine wet batter(s) to the dry batter. Then, gently stir in the apple cider vinegar.
  5. Fold in 1/2 cup of chopped apple into the batter (optional)
  6. Spoon the batter into lined muffin pans, filling each cup 2/3 of the way full.
  7. Topping – Place 3 Tablespoons of rolled oats and 1/4 to 1/3 cup chopped apple together in a bowl. Mix the oats and apples with 2 Tablespoons of coconut sugar or brown sugar substitute. Top the muffins with extra rolled oats and/or apple.
  8. Place the muffin tin in the oven for 18-22 minutes or until the center comes out clean with a toothpick.
  9. Remove and place the muffins on a cooling rack for 5 -10 minutes.


If you loosely cover muffins overnight on the counter or refrigerated, the liners peel off easily the next day, and the flavor and texture are even better.

Flourless Baking Tip – Weigh the oat flour after grinding oats to ensure it’s equivalent to 160 grams. Weight of rolled oats can vary depending on the cut of oats and brand. 

  • Category: Breakfast
  • Method: Baking
  • Cuisine: American


  • Serving Size: 1 muffin
  • Calories: 172
  • Sugar: 8.7 g
  • Sodium: 136.6 mg
  • Fat: 0.3 g
  • Saturated Fat: 0.4 g
  • Carbohydrates: 32.8 g
  • Fiber: 4.2 g
  • Protein: 4.5 g
  • Cholesterol: 0 mg

Keywords: gluten free, breakfast, muffins, snacks, apple muffins, vegan muffins

Of course, these healthy apple muffins are delicious any time but are especially tasty while apples are at their best. Do you have any seasonal recipes you make all year long? Let me know in the comments below! 




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