Gluten-Free Apple Muffins are soft and moist, packed with apples, oats, almond butter, and crunchy pecans, with no flour needed and just the right amount of sweetness.

Freshly baked gluten free apple muffins ready to be enjoyed.
chelsea

author’s note

The Muffins My Kids Actually Wake Up For!

Getting kids up, ready, and out the door for school or sports can feel like a full workout, but the biggest game-changer for me has been having grab-and-go breakfasts prepped ahead of time.

If your kids are anything like mine, they get hangry fast, and these gluten-free apple muffins save us every time. The kids love them, I love them, and they couldn’t be easier to make.

They’re packed with feel-good ingredients that keep everyone going all morning long, and I love knowing they’re starting the day with something wholesome. I’ve even tripled the batch and frozen extras. They defrost beautifully!

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Quick Tip

If you enjoy gluten-free recipes, be sure to try my other gluten-free muffin recipe — these Chocolate and Peanut Butter Muffins are one of the most popular recipes on this website!

Oat flour being made in a blender.

How To Make Oat Flour

If you have quick oats or old-fashioned oats, you can have oat flour for your gluten free apple muffins in minutes!

  1. Add the oats to a food processor or blender.
  2. Grind until it looks like flour.
  3. Stir to make sure everything is all blended and there aren’t any whole oats left.
  4. Measure the oat flour after grinding, not before, before you use it in the muffins.
Gluten free apple cinnamon muffins being made by adding wet and dry ingredients, mixing them together, adding the mixture to a muffin tin, and baking.

How To Make Gluten Free Apple Muffins

  1. Prep: Pre-heat oven. Grease 8 muffin cups and fill the empty cups halfway with water.
  2. Wet: Beat applesauce, almond butter, honey, vanilla, and sugar. Beat in the egg.
  3. Add Dry: Mix in salt, baking soda, baking powder, and oat flour. Stir in the whole oats.
  4. Fold In: Toss chopped apple with lemon, then stir it in with cinnamon and pecans.
  5. Bake & Cool: Divide batter among 8 cups, top with the last 2 tbsp pecans and bake.

Storage

  • Store leftover gluten free apple muffins in an airtight container at room temp for up to 3 days or in the fridge for up to a week.
  • To freeze, place fully cooled muffins in a freezer-safe bag or container and freeze for up to 3 months. Thaw at room temp or microwave for 15–30 seconds to warm.

More Muffin Recipes:

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4.72 from 7 votes

Gluten-Free Apple Muffins

Gluten-Free Apple Muffins are packed with wholesome goodness—almond butter, apples, oats, and pecans. Flourless, lightly sweetened, and loaded with flavor and texture!
Make sure to check all ingredient labels to verify all the products were prepared in a gluten-free facility, if gluten intolerance is a concern.
Prep Time: 15 minutes
Cook Time: 16 minutes
Total Time: 31 minutes
Servings: 8 muffins

Video

Ingredients

  • 1/2 cup unsweetened applesauce
  • 1/2 cup roasted and salted almond butter see note 1
  • 2 tablespoons honey
  • 1 teaspoon vanilla extract
  • 2 tablespoons brown sugar lightly packed, see note 2
  • 1 large egg
  • 1/4 teaspoon salt
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/3 cup + 1 tablespoon oat flour old-fashioned oats that have been blended—see note 3
  • 1/3 cup old-fashioned oats
  • 1/2 cup chopped tart apple I use Granny Smith
  • 1 teaspoon lemon juice
  • 1/2 teaspoon ground cinnamon
  • 4 tablespoons finely chopped pecans divided

Instructions 

  • Preheat oven to 350°F. Spray 8 cavities of a light-colored muffin pan with cooking spray and fill the other empty cavities halfway with water (ensures even baking). Do not use muffin liners—these muffins stick to the paper.
  • In a large bowl, using a hand mixer, beat the applesauce, almond butter (see note 1), honey, vanilla extract, and brown sugar (see note 2) in a large bowl. Beat in the egg until mixed in. Add salt, baking soda, baking powder, and oat flour (see note 3). Mix. Stir in the old-fashioned oats and mix to combine.
  • Peel the apple and chop into small pieces. In another small bowl, toss the chopped apple with the lemon juice. Add the apple pieces (and any accumulated liquid) to the muffin batter along with 2 tablespoons of chopped pecans and the ground cinnamon. Gently stir to combine.
  • Fill the 8 muffin cavities 3/4 full. All the batter should be used among the 8 cavities. Evenly sprinkle the last 2 tablespoons of pecans on the tops of the muffins. Bake at 350°F for 16–18 minutes or until lightly browned around the edges. Watch carefully; overbaking will make these muffins dry and less flavorful.
  • Let the muffins stand in the muffin pan for 5–10 minutes before gently coaxing them out with a spoon onto a cooling rack (while hot, these muffins have a tendency to crumble). Allow muffins to finish cooling on the cooling rack. Muffins are best enjoyed within 2–3 days.
Final step! Please let us know how it was by leaving a review.

Recipe Notes

Note 1: Use high-quality almond butter, ideally slow-roasted and sea-salted. Adjust sugar and salt if your almond butter is unsalted, and stir well if the almond butter has separated.
Note 2: If you want your muffins sweeter, increase brown sugar by 1–2 tablespoons. If you prefer sweeter treats, you’ll likely want to increase it by 2 tablespoons.
Note 3: Make sure to measure the oat flour after it’s been turned to flour and not in the original whole oat form.
 To make oat flour:
  1. Place the oats (old-fashioned or quick oats) in a food processor or small blender.
  2. Pulse the oats until they are ground into a powder-like consistency that resembles flour.
Storage: Store muffins in an airtight container at room temperature for 2–3 days. Muffins can be frozen for up to 2 months, individually and tightly wrapped in plastic wrap. Thaw at room temperature.

Nutrition

Serving: 1serving | Calories: 158kcal | Carbohydrates: 13g | Protein: 1.8g | Fat: 11.1g | Cholesterol: 47.8mg | Sodium: 11.1mg | Fiber: 0.9g | Sugar: 7.9g

Nutrition information is automatically calculated, so should only be used as an approximation.

Tips For Gluten Free Apple Muffins

  • Check that all ingredients are labeled gluten-free—they might be made in the same place as gluten.
  • Let the muffins sit and cool fully before eating—they can fall apart when hot.
  • Grease the muffin pan well (don’t use liners—they stick!). A good muffin pan really helps them come out clean.

Meet Chelsea


Hello, and welcome to Chelsea’s Messy Apron! I’m Chelsea, the recipe developer, food photographer, and writer behind the site. I’m passionate about creating simple, reliable, and delicious recipes that anyone can make.

Thanks for stopping by—I hope you find something delicious to make!

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54 Comments

  1. Kristine @ Kristine's Kitchen says:

    These apple muffins look perfect for this time of year! I love baking with almond butter and oat flour and will have to try these soon!

  2. marcie says:

    These muffins are perfection! I haven’t made flourless muffins in too long, and I love these flavors. These need to happen soon! Pinning. 🙂

  3. Kelly says:

    5 stars
    I wasn’t always a fan of nuts in baked goods but now I love them – especially in muffins 🙂 These look absolutely delicious! Love the almond butter in here and the fact that they are healthy – that means I can have more right?? 🙂 Pinning of course and hope you have a great rest of the weekend sweet lady!

    1. chelseamessyapron says:

      You are the sweetest Kelly!! Thanks so much; I hope you have a great Sunday!

  4. Medeja says:

    I would love few for breakfast..

  5. Michele @ Two Raspberries says:

    these look delicious! pinning these 😉 i love how healthy and the flavor combo YUM!

  6. Bianca @ Confessions of a Chocoholic says:

    I love nuts in baked goods and these muffins sound pretty perfect to me! Bonus points that they are healthy!

    1. chelseamessyapron says:

      Thanks so much Bianca!

  7. Ashley says:

    I love nuts in baked goods so that doesn’t bother me! These look fantastic! And I love that you have almond butter in them too – my favorite! Hope you’re having a great weekend!

    1. chelseamessyapron says:

      Thanks Ashley!! Isn’t almond butter the best?! Hope you are too 🙂

  8. Shela says:

    What type of oats are you using? I’m new to this and am not sure.
    Thank you!

    1. chelseamessyapron says:

      Just regular old fashioned oats that I blended in my blender 🙂 hope that helps!!

  9. Meg @ The Housewife in Training Files says:

    I most definitely do not like nuts in my baked goods but for some reason I do like them in muffins and breads as well! I am craving one of this lil muffins with my morning coffee right meow. Pinned!

  10. Baby June says:

    Oooh those look delicious! Love how healthy they are, I would definitely love one (or two) of these for breakfast : )

    1. chelseamessyapron says:

      Thanks so much 🙂

      1. Erin says:

        Can you substitute flour for oats? what would the ratio be?