Apple Yogurt Muffins

VG

These apple yogurt muffins are studded with apples and packed with cinnamon flavor. They’re soft, fluffy and extra moist thanks to the Greek yogurt.

Today I’m sharing the fourth and final variation of my yogurt muffins! I’ve already shared blueberry yogurt muffins, strawberry yogurt muffins and chocolate chip yogurt muffins and now I have an apple version for you!

Apple picking is definitely one of my favorite fall activities and I love using them to make tasty baked goods like these apple yogurt muffins. They’re soft, moist and have the perfect amount of sweetness from the maple syrup and apple chunks. Plus, they have added protein thanks to the Greek yogurt, making them more filling than most muffin recipes.

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Why You’ll Love This Recipe

  • These apple yogurt muffins are protein-packed which means you won’t be hungry 10 minutes after eating one!
  • They’re made with simple ingredients you likely already have in your kitchen.
  • They’re perfect for meal prep. I love making a batch over the weekend to have on hand for breakfast or a snack throughout the week!
Ingredients measured out to make apple yogurt muffins: whole wheat pastry flour, cinnamon, Greek yogurt, sea salt, maple syrup, eggs, baking powder, coconut oil, vanilla, almond milk, baking soda and chopped apples.

Ingredients Needed

  • whole wheat pastry flour – whole wheat pastry flour works better than regular whole wheat flour if you’re looking for the light and fluffy texture that regular all-purpose flour provides, but still want the nutrients of whole wheat flour. My go-to brand is Bob’s Red Mill whole wheat pastry flour. If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • baking powder and baking soda – to help the muffins rise.
  • sea salt – balances the flavors of the muffins.
  • cinnamon – a perfect pairing with apples and nice warming spice for these muffins.
  • eggs – helps bind the ingredients together and provide structure for the muffins.
  • Greek yogurt – Greek yogurt keeps these muffins moist without a lot of added oil. I recommend using plain whole milk (full fat) yogurt for the best results.
  • coconut oil – helps keep these muffins super moist and fluffy.
  • maple syrup – I love using maple syrup as the natural sweetener in these muffins, but I bet honey or even a sugar alternative like stevia or monk fruit would work fine as a substitute.
  • unsweetened almond milk – I used unsweetened almond milk, but any type of milk will work, including cow’s milk.
  • vanilla extract – a flavor enhancer.
  • apples – you’ll need about 1-2 apples, depending on size. You can peel the apples (or not). Either way, you’ll want to chop them into small pieces.
Four photos showing the process of making the batter for apple yogurt muffins.

How to Make Apple Yogurt Muffins

Step 1: Start by combining the dry ingredients. In a large bowl, mix the flour, baking powder, baking soda, salt and cinnamon.

Step 2: In a medium mixing bowl, whisk the eggs, yogurt, oil, maple syrup, almond milk and vanilla extract. Add the wet ingredients to the dry ingredients and stir with a spoon until just combined. Make sure you don’t over-mix or the muffins will be too dense after baking. Fold in the apple chunks.

Step 3: Line a muffin tin with paper or silicone muffin liners. Evenly divide the muffin batter into the prepared muffin tin. Sprinkle extra apple chunks on top.

Step 4: Bake at 400ºF for 16-18 minutes or until a toothpick inserted into the center of the muffin comes out clean. Let the muffins cool for a few minutes in the pan and then let cool completely on a wire rack.

Overhead view of apple yogurt muffins scattered around with an apple.

What Types of Apples Are Best to Bake With?

Typically, I like to use a mix of apples that are sweet but tart and firm so that it holds up well to baking – if apples get mushy while baking, it’s a no-go for me! Honeycrisp, Pink Lady, and Granny Smith are fantastic apples to bake with.

Two apple yogurt muffins stacked on top of each other. There are more muffins scattered around as well as whole apples.

Tips For Success

  • It’s important to make sure you’re using room temperature milk, eggs, maple syrup and yogurt! If any of these ingredients are cool, the coconut oil will solidify and create clumps. If you notice this happening, you can set the mixing bowl on the warm part of your stovetop as the oven preheats or set the mixing bowl in a larger bowl of hot water until the coconut oil melts again. You just want to make sure you don’t get the batter too hot or the eggs will start cooking. Here’s a guide for how to bring things like butter, eggs and yogurt to room temp.
  • When combining your dry and wet ingredients make sure you mix until just combined and don’t over-mix otherwise your muffins could turn out too dense or rubbery. It’s even okay if there are a few streaks of flour remaining as they’ll get mixed in when you stir in the apples.
  • I highly recommend using silicone muffin liners or baking cups for the best results and to prevent the muffins from sticking.
  • Let the muffins cool for a few minutes in the muffin tin and then remove to let cool completely on a wire rack. Don’t leave the muffins in the muffin tin for too long because they’ll continue to bake and could dry out!
  • If using paper cupcake liners, make sure to let the muffins cool completely before trying to remove the liners otherwise your muffins will likely stick.
Baked apple yogurt muffins in a muffin tin.

Frequently Asked Questions

Can I use all-purpose flour?

Yes! All-purpose flour will work just fine in place of whole wheat pastry flour.

Can I make these muffins gluten-free?

I haven’t tested a gluten-free version of these muffins, but I would imagine using a 1:1 gluten-free all-purpose flour would work just fine in place of the whole wheat pastry flour. My favorite brand is Bob’s Red Mill gluten-free 1:1 all-purpose flour.

How can I make these muffins dairy-free?

I haven’t tried it, but I would imagine using a non-dairy Greek-style yogurt or really any vegan yogurt would work just fine as a substitute for the Greek yogurt.

Is there an egg substitute?

I haven’t tested an egg-free version of these muffins, but let me know if you decide to experiment in the comments below! I would imagine using two flax eggs or chia eggs in place of the regular eggs would work just fine. If you’re looking for a vegan apple recipe I do have a vegan apple bread recipe you could try instead!

Can I swap the apples for a different mix-in?

Totally! Feel free to make this recipe your own and customize the mix-ins. You can also try my strawberry yogurt muffins, blueberry yogurt muffins or chocolate chip yogurt muffins!

How do I prevent my muffins from sticking to the liners?

I recommend using silicone muffin liners or baking cups for the best results and to avoid the muffins from sticking too much. I also recommend spraying your liners with a little cooking spray. Also, make sure to let your muffins cool completely before trying to remove the liners otherwise they could stick. If you want, you can pop the muffins in the fridge to cool for an hour or so before removing the liners.

What type of yogurt is best to use?

I recommend using plain whole-milk Greek yogurt for this recipe. It’s what keeps these muffins moist and adds some protein. My go-to yogurt brands are Fage 5% plain Greek yogurt and Siggi’s plain whole milk yogurt. 2% Greek yogurt will also work, but I don’t recommend using non-fat Greek yogurt as it won’t add as much moisture to the muffins and it sometimes has fillers which could change the consistency.

Three apple yogurt muffins stacked on top of each other. There are other muffins scattered around with apples.

How to Store Apple Yogurt Muffins

After allowing the muffins to cool completely, store them in an airtight container for 3-4 days at room temperature or for up to 1 week in the refrigerator. For longer storage, you can freeze these muffins for up to 3 months in a freezer-safe container or bag. I like to use my Stasher bags for easy storage. To defrost, place muffins in the fridge overnight, at room temperature or defrost in the microwave.

More Muffin Recipes

Be sure to check out all of my apple recipes as well as the full collection of muffin recipes here on EBF!

Apple Yogurt Muffins

5 from 1 vote
These apple yogurt muffins are studded with apples and packed with cinnamon flavor. They're soft, fluffy and extra moist thanks to the Greek yogurt. Perfect for meal prep!
Three apple yogurt muffins stacked on top of each other. The muffins are wrapped in paper liners.
Prep Time 10 minutes
Cook Time 18 minutes
Total Time 28 minutes
Servings 12

Ingredients

Instructions
 

  • Preheat oven to 400°F. Place 12 paper or silicone liners in your muffin tin.
  • In a large bowl, combine flour, baking powder, baking soda, salt and cinnamon.
    Mixing together flour, baking powder, baking soda, salt and cinnamon.
  • In a medium mixing bowl, whisk together eggs, Greek yogurt, oil, maple syrup, almond milk and vanilla extract.
  • Pour the liquid mixture into the bowl with the dry ingredients and stir until mixture is just combined. Don’t over-mix! It’s okay if there are a few streaks of flour left.
    Adding wet ingredients to dry ingredients.
  • Fold in apple chunks.
    Folding in apples into the yogurt muffin batter.
  • Evenly divide the batter into the prepared muffin tins.
    Apple yogurt muffin batter divided into muffin tin with paper liners.
  • Bake for 16-18 minutes or until a toothpick inserted in the center of the muffin comes out clean.
    Twelve baked apple yogurt muffins in a muffin tin.
  • Let muffins cool in the tin for a few minutes, then remove so they don’t continue to cook and let cool completely on a wire rack.
  • Store at room temperature for 3-4 days or in the refrigerator for up to 1 week in an airtight container. You can also freeze for up to 3 months in a freezer-safe container.

Equipment

Notes

  • Whole wheat pastry flour: If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour.
  • Greek yogurt: I haven’t tried it, but I bet using a vegan yogurt would work just fine! 
  • Maple syrup: You can use agave, honey or even monk fruit maple syrup as a substitute for maple syrup. 
  • Almond milk: Any dairy-free or dairy milk will work in this recipe.

Nutrition

Serving: 1muffin Calories: 209kcal Carbohydrates: 33g Protein: 6g Fat: 7g Saturated Fat: 5g Monounsaturated Fat: 1g Cholesterol: 34mg Sodium: 182mg Potassium: 56mg Fiber: 4g Sugar: 10g
Course: Breakfast
Cuisine: American
Keyword: apple yogurt muffins

DID YOU MAKE THIS RECIPE?

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Recipe Rating




    4 comments
    1. Kathy
      August 18, 2022 AT 8:17 pm

      Would sorghum flour work? I can’t have wheat/gluten.

      1. Brittany Mullins
        August 19, 2022 AT 2:39 pm

        Hey Kathy – I am not sure how sorghum flour would work with these muffins. If you’re looking for a gluten-free substitute I’d recommend using a gluten-free all-purpose 1:1 baking flour. Let me know how they turn out if you end up trying them!

    2. Angela
      June 9, 2022 AT 9:26 am

      5 stars
      I often bake muffins, but I have never baked them with whole grain flour. I’ll try to cook if I find such flour. Thanks for the helpful recipe!

      1. Brittany Mullins
        June 9, 2022 AT 10:11 am

        Hi Angela, you’ll have to come back and let me know how it goes! If you can’t find whole wheat pastry flour you can also use white whole wheat flour, a blend of all-purpose and regular whole wheat flour or just regular all-purpose flour too.

Parchment paper lined with protein balls.

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