Gluten-Free Apple Muffins (With Protein!)
This website uses affiliate links which may earn commission for purchases made at no additional cost to you.
These Protein Gluten-Free Apple Muffins make the perfect healthy snack! Made with Greek yogurt, fresh apples, and oat flour, they’re kid-approved, meal-prep friendly, and keep energy levels stable between meals.
We have been loving these Gluten-Free Apple Muffins to add to our balanced breakfast before school or to have as an afterschool snack. These gluten free muffins are high in protein and are naturally sweetened with apples and a small amount of maple syrup. The warm apple cinnamon flavor is delicious and makes the house smell so good!
I personally love that they’re low in sugar and high in protein. I like to bake a batch of these over the weekend, so we have quick snacks ready to go for busy weeks for lunchboxes, sports, and after school.
I love prepping Gluten-Free Protein Carrot Cake Muffins and Blender Blueberry Muffins for an easy grab-and-go snack as well!
Recipe Ingredients
You’ll need the following ingredients to make these Gluten Free Apple Cinnamon Muffins:
Ingredient Notes
- Oat Flour: I make my own by blending Gluten-Free Rolled Oats (I get my gluten-free oats from Trader Joe’s) in a high-speed blender for about 15-20 seconds. This creates a lighter texture than store-bought oat flour. You can use store-bought oat flour, your muffins just may come out denser.
- Greek Yogurt: The Greek yogurt adds moisture and a protein boost to these muffins, making them more filling than your average muffin. I use full-fat yogurt, but you can use low-fat or non-fat instead.
- Apples: Using both grated and diced apples gives these muffins the perfect texture – the grated apple melts into the batter, providing moisture and sweetness, while the diced pieces give bursts of apple flavor in every bite. Feel free to just stick to one method of prepping the apples if desired (either all diced or all grated).
Additions & Substitutions
- Mix-ins: Try adding chopped walnuts, pecans, or even a handful of raisins for texture variation.
- Greek Yogurt: You can substitute with dairy-free yogurt if needed, though the protein content may be slightly lower. You can also use a low-fat or non-fat Greek yogurt or a regular plain yogurt.
- Sweetener: The recipe uses maple syrup, but honey would work well too if you prefer. The recipe calls for 1/4 cup maple syrup – if you want them to be a little sweeter, try using 1/3 cup maple syrup. I find that they’re sweet enough with 1/4 cup, but I am used to eating lower sugar overall. Either way is fine!
Tools For This Recipe
- Mixing bowls
- High-speed blender (to blend the oats, if needed)
- Grater (to grate the apple)
- Muffin tin
How to Make Gluten-Free Apple Muffins: Step-by-Step
For the full recipe with the exact ingredients, scroll down to the printable recipe card below!
Step 1: In a large bowl, mix blended oats (oat flour), baking powder, baking soda, and cinnamon.
Step 2: Prepare your apples – grate one apple and dice the other apple into small pieces. Reserve a handful of the chopped apples to top the muffins with. In a medium bowl, whisk together shredded apples, diced apples, eggs, Greek yogurt, maple syrup, and vanilla extract.
Step 3: Add the wet ingredients to the dry ingredients and stir until just combined.
Step 4: Use a cookie scoop or a spoon to scoop the muffin batter into a lined muffin tin, filling each liner to the brim. Bake at 375°F for 15-18 minutes or until a toothpick inserted into the middle of a muffin comes out clean.
Recipe Tips & Tricks
- Grating Technique: Use the large holes on a box grater for the grated apple – this gives the perfect texture without making the batter too wet.
- Don’t Overmix: Stop stirring as soon as the ingredients are combined to ensure tender muffins.
- Muffin Liners: Use parchment paper liners or silicone liners for easy removal – these muffins can stick to regular paper liners.
Storage & Reheating
- Countertop: Store in an airtight container for up to 2 days.
- Fridge: Keep fresh for up to 5 days in an airtight container.
- Freezer: Freeze for up to 3 months. Simply thaw overnight in the refrigerator or microwave for 20-30 seconds from frozen when ready to eat!
Frequently Asked Questions
Yes! You can substitute the Greek yogurt with a dairy-free yogurt alternative. The protein content might be slightly lower, but the texture should be similar.
Each muffin contains approximately 4-5 grams of protein, coming primarily from the eggs and Greek yogurt, but also from the oats.
Absolutely! Though I much prefer freshly ground oat flour as it produces a lighter texture, pre-made oat flour works well, too. Your muffins may come out more dense if using store-bought oat flour.
Yes! If you don’t want to cut and grate your apples (though you’ll be surprised that this actually doesn’t take very long!), just choose one way (dice both apples or grate both apples).
In a Lunch Rut?
Grab your FREE 10-Day Lunchbox Recipe Meal Plan! Great for adults and kids!
More Muffin Recipes You’ll Love!
Did you try this recipe?
Let me know how you liked it by leaving a comment and rating below! Or tag me on Instagram and share what you made!
Gluten-Free Apple Muffins (With Protein!)
Ingredients
- 2 cups gluten-free oats, blended into flour* (I use Trader Joe’s Gluten-Free Rolled Oats)
- 2 teaspoons baking powder
- 1 teaspoon baking soda
- 2 teaspoons cinnamon
- 2 apples, 1 apple grated and 1 apple diced
- 2 eggs
- ½ cup Greek yogurt, I used full-fat, but any kind will do
- ¼ cup 100% pure maple syrup
- 2 teaspoons vanilla extract
Instructions
- Preheat oven to 375 degrees Fahrenheit. Line a muffin tin with non-stick liners and set aside.
- In a large bowl, mix blended oats (oat flour* – see notes), baking powder, baking soda, and cinnamon.
- Prepare your apples – grate one apple and dice the other apple into small pieces. Reserve a handful of the chopped apples to top the muffins with.
- In a medium bowl, whisk together shredded apples, diced apples, eggs, Greek yogurt, maple syrup, and vanilla extract.
- Add the wet ingredients to the dry ingredients and stir until just combined.
- Use a cookie scoop or a spoon to scoop the muffin batter into muffin liners, filling each liner to the brim. Top muffins with reserved diced apple pieces. Bake for 15-18 minutes or until a toothpick inserted into the middle of a muffin comes out clean.
Super easy to make! They were delicious. The whole family loves them! Bonus: our house smelled incredible.
Hi Jen! I’m so happy to hear these muffins were a hit with the whole family and that they made the house smell good! Thanks so much for taking the time to leave a review! 🙂
Amazing. I love them and my son loves them. And they are healthy!
Hi Ryan! Yay! I’m so happy to hear that you and your son love the muffins!! Thank you so much for taking the time to leave a review. I really appreciate it! 🙂
These muffins made my kitchen smell delicious! They also look beautiful coming out of the oven. I took the recommendation to warm them up and add some butter and they were so tasty! I heated mine for about 20 seconds.
I was initially hesitant to make this recipe because you have to grate and apple and chop another. I know that doesn’t sound like a lot but I’m all about quick recipes. Honestly, it took no time at all to do either of those things. I like the texture you get from the oat flour in these as well. It’s less bready or stodgy than regular flour muffins which I usually find too dry. These are definitely moist but not too moist. Next time I may try them with some melted peanut butter drizzled on top!
Hi Lexi! Aww, yay! I’m so happy that you enjoyed these muffins! I’m glad you tried the recipe as is and discovered that it didn’t take much time to grate and chop the apples. Melting some peanut butter on them next time sounds delicious! Thank you so much for taking the time to leave a review!