Best Apple Cinnamon Muffins with Greek Yogurt Recipe

Posted on November 15, 2025

It was a crisp autumn morning when I first baked these apple cinnamon muffins. The leaves were just starting to turn, and the smell of apples and cinnamon wafting through my kitchen was pure magic. These muffins are like a hug in food form—soft, fluffy, and with just the right amount of sweetness. And the secret ingredient? Greek yogurt. Not only does it make them extra moist, but it adds a little protein boost, so I feel good about having one (or two!) for breakfast.

If you’re anything like me and can never resist the combination of apples and cinnamon, this recipe is going to be on repeat all season long. Let’s bake something cozy, shall we?

Why You’ll Love These Apple Cinnamon Muffins

Let me tell you, these muffins have completely spoiled store-bought ones for me. Once you’ve tasted the real deal, it’s hard to go back! Here’s why I think you’re going to love them too:

Soft and moist texture: Thank you, Greek yogurt! It’s the secret to tender muffins that stay fresh for days.
Warm, cozy flavors: The combination of cinnamon and fresh apples is like fall in every bite.
Easy to make: No fancy equipment needed—just a bowl, a whisk, and your trusty muffin tin.
Healthier than most muffins: Less butter, more natural sweetness from the apples, and a little protein boost from the yogurt. It’s indulgence you can feel good about.

These muffins are perfect for breakfast, a mid-morning snack, or even dessert. I’ve brought these to potlucks and brunches, and they’re always the first to disappear!

What Ingredients You’ll Need

One of the best things about this recipe is that you probably already have most of these ingredients in your kitchen. Here’s what you’ll need to make these cozy apple cinnamon muffins:

For the Muffin Base:

All-purpose flour (1 ¾ cups / 220g) – The base of our muffins. You can substitute whole wheat flour for a denser muffin, but I love the fluffiness of all-purpose.
Baking powder (1 ½ tsp) – Gives our muffins that perfect rise.
Baking soda (½ tsp) – Works with the yogurt to make the muffins light and airy.
Salt (½ tsp) – Don’t skip it! It balances the sweetness.

For the Wet Ingredients:

Greek yogurt (1 cup / 240g) – Full-fat or 2% works best. It keeps the muffins moist and adds a nice tangy flavor.
Eggs (2 large) – These help bind everything together. Room temperature eggs work best!
Unsalted butter (¼ cup / 60g, melted) – Adds richness without being too heavy.
Brown sugar (½ cup / 100g) – For that deep, caramel-like sweetness.
Granulated sugar (¼ cup / 50g) – Adds a touch of extra sweetness and helps the muffins brown beautifully.
Vanilla extract (1 tsp) – Adds a lovely depth of flavor.

For the Star Ingredients:

Apples (2 medium, peeled and diced) – I like to use Honeycrisp or Granny Smith for their balance of sweetness and tartness.
Cinnamon (1 tsp) – The warm spice that ties everything together.

Quick tip: If you’re feeling fancy, sprinkle a little cinnamon sugar on top of the muffins before baking for a sweet, crunchy topping!

Equipment Needed

You don’t need a fully stocked kitchen to whip up these muffins. Here’s what you’ll need:

Muffin tin: A standard 12-cup muffin tin works perfectly.
Mixing bowls: One for wet ingredients, one for dry. I use my biggest bowl for the wet ingredients since everything gets mixed together there.
Whisk or hand mixer: I usually go for a whisk—it’s easier to clean, and this recipe doesn’t require heavy mixing.
Measuring cups and spoons: Baking is all about precision, so don’t skip these!
Rubber spatula: For scraping every last bit of batter out of the bowl.

That’s it! No fancy gadgets here.

How to Make Apple Cinnamon Muffins: Step-by-Step

Ready to bake? Let’s do this! Follow these steps, and you’ll have warm, cozy muffins in no time.

Preheat your oven: Set it to 375°F (190°C). Line your muffin tin with paper liners or lightly grease with cooking spray.
Prepare your apples: Peel and dice the apples into small, bite-sized pieces. Set aside.
Mix the dry ingredients: In a medium bowl, whisk together the flour, baking powder, baking soda, cinnamon, and salt. This ensures everything is evenly distributed.
Combine the wet ingredients: In a large bowl, whisk together the Greek yogurt, melted butter (cooled slightly), eggs, brown sugar, granulated sugar, and vanilla extract. Whisk until smooth and creamy.
Bring it all together: Slowly add the dry ingredients to the wet ingredients, folding gently with a spatula. Be careful not to overmix—just stir until no streaks of flour remain.
Fold in the apples: Gently fold the diced apples into the batter. They’ll add little pockets of sweetness to each muffin.
Fill the muffin tin: Divide the batter evenly among the muffin cups. Each should be about ¾ full.
Bake: Pop the muffins into the oven and bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean. Your kitchen will smell amazing!
Cool and enjoy: Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely (if you can wait that long!).

Pro tip: If you want crispier muffin tops, bake at 400°F (205°C) for the first 5 minutes, then reduce the temperature to 375°F (190°C) for the remaining time.

My Best Tips & Techniques

Here are a few tricks I’ve learned from making these muffins more times than I can count:

Don’t overmix: Once you add the dry ingredients, stir just until combined. Overmixing can make your muffins dense instead of fluffy.
Room temperature ingredients: Let your yogurt and eggs come to room temp before mixing. It makes for a smoother batter.
Use fresh, crisp apples: The apples are the star here, so choose ones that are firm and flavorful. Honeycrisp and Granny Smith are my favorites.
Make them prettier: Sprinkle some turbinado sugar on top of the muffins before baking for a bakery-style look and a delightful crunch.

Ways to Mix It Up

Once you’ve mastered the basic recipe, here’s how you can get creative:

Nutty Apple Muffins: Stir in ½ cup chopped walnuts or pecans for added crunch.
Caramel Apple Muffins: Add a drizzle of caramel sauce on top of the batter before baking. Trust me, it’s a game-changer.
Spiced Up: Add a pinch of nutmeg and cloves for extra warmth.
Vegan Version: Use plant-based yogurt and flax eggs (1 tbsp flaxseed meal + 3 tbsp water per egg).
Gluten-Free: Swap the all-purpose flour for a 1:1 gluten-free baking blend. It works beautifully!

Serving Ideas & Storage

Serving Suggestions:

Enjoy warm with a pat of butter.
Pair with a hot cup of coffee or tea for the ultimate cozy treat.
For an indulgent dessert, serve with vanilla ice cream and a drizzle of caramel.

Storage Tips:

Room temperature: Store in an airtight container for up to 3 days.
Refrigerator: These muffins keep well in the fridge for up to a week. Just pop one in the microwave for 15 seconds to warm it up.
Freezer: Freeze in an airtight container for up to 3 months. Reheat in the microwave or oven for a quick breakfast or snack.

Nutritional Info & Health Benefits

Here’s why these muffins are a bit better for you than your average bakery muffin:

Nutritional Info (per muffin)	Amount
Calories	190
Protein	6g
Carbs	30g
Fat	5g
Fiber	2g

Health Highlights: Greek yogurt adds protein, apples bring natural sweetness, and the muffins are lower in sugar than most store-bought options. It’s a treat you can feel good about!

Final Thoughts

So there you have it—my cozy apple cinnamon muffins with Greek yogurt! This recipe has become a staple in my home, especially during the cooler months. They’re easy to make, smell incredible, and taste even better.

Make them your own by trying the variations or adding your favorite mix-ins. I can’t wait to hear how yours turn out!

If you give these a try, let me know in the comments below or tag me on Instagram @yourhandle—I love seeing your creations. Happy baking!

FAQs

Q: Can I use regular yogurt instead of Greek yogurt?

A: Yes, but the texture might be a little less creamy. If you’re using regular yogurt, try straining it first to get a thicker consistency.

Q: What kind of apples work best?

A: I love using Honeycrisp or Granny Smith because they hold their shape well and have a nice balance of sweet and tart. But really, any apple will work!

Q: Can I make these muffins ahead of time?

A: Absolutely! These keep beautifully. Store them in an airtight container, and they’ll stay fresh for up to 3 days at room temperature or a week in the fridge.

Q: How do I make these muffins dairy-free?

A: Use a dairy-free yogurt like coconut or almond-based yogurt and swap the butter for coconut oil or a plant-based alternative.

Q: Can I make mini muffins with this batter?

A: Definitely! Use a mini muffin tin and reduce the baking time to 10-12 minutes. Perfect for little hands or a party platter!

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