Apple Cinnamon Greek Yogurt Muffins

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There’s something about the scent of warm apples and cinnamon wafting through the kitchen that makes me feel instantly cozy. These Apple Cinnamon Greek Yogurt Muffins have quickly become one of my go-to bakes during the cooler months. They’re soft, moist, and packed with chunks of sweet apple in every bite—everything you want in a homemade muffin. The addition of Greek yogurt makes them extra tender and adds a subtle tang that balances out the sweetness perfectly.

I’ve baked countless batches of these muffins for breakfast, snacks, and even lazy weekend brunches. They’re easy to whip up with pantry staples, and they always disappear fast. Whether you’re making them for a crowd or just to enjoy with a cup of coffee, these muffins never disappoint.

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Why You’ll Love These Apple Cinnamon Greek Yogurt Muffins

These muffins check all the boxes: they’re fluffy, flavorful, and secretly a little better-for-you thanks to the protein-rich Greek yogurt. The cinnamon-sugar topping gives them a bakery-style finish, and the tender apple chunks melt in your mouth. They’re the kind of treat that feels indulgent but isn’t overly sweet, making them perfect for any time of day.

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What Kind of Apples Work Best for These Muffins?

You’ll want apples that hold their shape while baking and have a nice balance of sweet and tart. I personally love using Honeycrisp or Fuji apples for that juicy sweetness, but Granny Smith also works well if you prefer a bit more tang. You can even mix two varieties for more depth of flavor.

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Options for Substitutions

Not a fan of Greek yogurt? Swap it out for sour cream or even a thick plant-based yogurt if you’re keeping it dairy-free. You can also use whole wheat flour for a heartier muffin, or toss in some chopped nuts like walnuts or pecans for added crunch. If you’re cutting down on sugar, coconut sugar or maple syrup are excellent natural alternatives.

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Ingredients for This Apple Cinnamon Greek Yogurt Muffins Recipe

• All-purpose flour – Gives the muffins structure and a tender crumb.
• Baking powder – Helps the muffins rise and stay fluffy.
• Baking soda – Reacts with the yogurt for additional lift.
• Salt – Enhances all the other flavors.
• Ground cinnamon – The star spice that pairs perfectly with apple.
• Unsalted butter – Adds richness and moisture.
• Granulated sugar – Sweetens the muffins and balances the tang from the yogurt.
• Eggs – Binds the ingredients and gives the muffins structure.
• Vanilla extract – Adds depth and warmth to the flavor.
• Greek yogurt – Makes the muffins ultra-moist and adds a protein boost.
• Apples – Freshly chopped, they add sweetness, texture, and that classic apple flavor.
• Brown sugar + cinnamon (for topping) – Creates a caramelized, lightly crisp top.

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Step 1: Prep Your Ingredients

Start by preheating your oven to 375°F (190°C) and lining a muffin tin with paper liners. Peel and finely chop 1-2 apples (about 1 1/2 cups). Set them aside. Melt the butter and let it cool slightly.

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Step 2: Mix the Dry Ingredients

In a medium bowl, whisk together the flour, baking powder, baking soda, salt, and cinnamon. Mixing these dry ingredients first ensures even distribution throughout the batter.

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Step 3: Combine the Wet Ingredients

In a large mixing bowl, whisk together the melted butter, granulated sugar, eggs, vanilla extract, and Greek yogurt until smooth and well combined.

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Step 4: Bring It All Together

Gradually fold the dry ingredients into the wet ingredients using a spatula or wooden spoon. Stir until just combined; don’t overmix. Gently fold in the chopped apples.

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Step 5: Fill the Muffin Tins

Scoop the batter into the lined muffin cups, filling each about 3/4 of the way. Sprinkle the top of each muffin with a mixture of brown sugar and cinnamon.

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Step 6: Bake

Place the muffin tin in the preheated oven and bake for 18–22 minutes, or until a toothpick inserted in the center comes out clean. Let the muffins cool in the tin for 5 minutes, then transfer them to a wire rack to cool completely.

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How Long to Prepare the Apple Cinnamon Greek Yogurt Muffins

Prep Time: Prepping these muffins is quick and easy. Chopping the apples, measuring out ingredients, and mixing everything together takes about 15–20 minutes. If you’re using pre-chopped apples or prepping in advance, you could cut this time down even more.

Bake Time: These muffins bake beautifully in about 18–22 minutes. You’ll know they’re done when the tops are golden and a toothpick inserted in the center comes out clean. Cooling time on a rack takes another 10–15 minutes, although they’re delicious slightly warm.

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Tips for Perfect Apple Cinnamon Greek Yogurt Muffins

• Use room-temperature eggs and yogurt to help the batter mix more evenly.
• Don’t overmix the batter—stir until just combined to keep the muffins tender.
• Dice the apples small for better distribution and even baking.
• Sprinkle extra cinnamon sugar on top before baking for a bakery-style finish.
• Let muffins rest in the tin for just 5 minutes before moving to a rack, so they don’t get soggy bottoms.

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Watch Out for These Mistakes While Cooking

• Using too much flour – Always spoon and level flour; don’t scoop directly with the measuring cup.
• Skipping the cinnamon sugar topping – It adds amazing flavor and texture.
• Overbaking – This will dry them out. Start checking at the 18-minute mark.
• Too large apple chunks – They can sink or stay crunchy. Aim for a fine dice.
• Not greasing liners – Even with paper liners, a light spray helps prevent sticking.

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What to Serve With Apple Cinnamon Greek Yogurt Muffins?

1. Fresh Fruit Salad

A mix of berries, melon, and grapes pairs beautifully with the warm spices of the muffins.

2. Scrambled Eggs or Omelet

Add protein and balance with something savory on the side.

3. Hot Coffee or Spiced Tea

These muffins are best enjoyed with a warm cup of something cozy.

4. Greek Yogurt Parfait

Layer with honey and granola for a satisfying, wholesome breakfast.

5. Maple Glazed Bacon

The salty-sweet contrast is perfect alongside these muffins.

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Storage Instructions

Room Temperature: Store cooled muffins in an airtight container for up to 2 days. They stay moist thanks to the yogurt.

Refrigerator: For longer storage (up to 5 days), keep them in the fridge. Just let them come to room temp or warm slightly before eating.

Freezer: These muffins freeze well! Wrap individually in plastic wrap and place in a freezer-safe bag. They’ll keep for up to 3 months. Thaw overnight or microwave for about 30 seconds.

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Estimated Nutrition (per muffin)

• Calories: 190–210
• Protein: 5g
• Carbohydrates: 28g
• Sugar: 14g
• Fat: 7g
• Saturated Fat: 4g
• Fiber: 2g
• Sodium: 160mg

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Frequently Asked Questions

How do I make these muffins gluten-free?

Use a 1:1 gluten-free flour blend in place of all-purpose flour. Make sure your baking powder is gluten-free too.

Can I use applesauce instead of chopped apples?

You can replace half the chopped apples with applesauce for added moisture, but don’t skip the chunks entirely—they give the best texture.

Are these muffins freezer-friendly?

Absolutely. Let them cool completely, wrap well, and freeze for up to 3 months.

Can I make these muffins ahead of time?

Yes! You can bake them a day ahead. They taste even better the next morning.

What’s the best way to reheat them?

Pop one in the microwave for 10–15 seconds or warm in a low oven at 300°F for 5–7 minutes.

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Conclusion

Apple Cinnamon Greek Yogurt Muffins are everything you want in a homemade treat—moist, spiced just right, and loaded with real apple pieces. Whether you’re baking for your family or treating yourself to a cozy morning, this recipe delivers comfort and satisfaction in every bite. And thanks to the Greek yogurt, you’re sneaking in a bit of nutrition, too. Warm, fluffy, and full of fall flavor, these muffins are worth making on repeat.

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