Samantha If there’s one thing I reach for when I want something sweet, comforting, and nourishing—it’s these Apple Cinnamon Greek Yogurt Muffins. These little golden gems are packed with protein, fiber, and warm cinnamon spice, and they’re made extra moist thanks to Greek yogurt. Whether you’re rushing out the door with a muffin in hand or cozying up with coffee on the weekend, these muffins hit the sweet spot every single time.
And the best part? These Apple Cinnamon Greek Yogurt Muffins check all the boxes: high-protein, low-oil, freezer-friendly, and kid-approved. They’re naturally sweetened, loaded with cozy fall flavor, and stay tender for days. I developed this recipe to help balance clean nutrition with serious comfort food cravings—and it quickly became one of my go-to healthy muffin meal prep ideas.
They’re a top pick for meal preppers, low-sugar snackers, and anyone looking to enjoy baked goods without all the guilt. Plus, thanks to the power of Greek yogurt, you’re getting calcium, probiotics, and an extra dose of protein in every bite according to the Cleveland Clinic. Let’s bake!
Apple Cinnamon Greek Yogurt Muffins – Moist, High-Protein Muffins for Easy Breakfast Meal Prep
Ingredients
- 1 cup plain Greek yogurt nonfat or full-fat
- 2 medium apples peeled and finely diced
- 1 ½ cups whole wheat flour
- 2 large eggs
- ⅓ cup honey or maple syrup
- 2 tbsp olive oil
- 1 tsp baking soda
- ½ tsp baking powder
- 1 ½ tsp cinnamon
- ¼ tsp nutmeg
- 1 tsp vanilla extract
- Pinch of salt
Instructions
- Step 1: Preheat and PrepPreheat oven to 350°F (175°C). Line or grease a muffin tin.
- Step 2: Mix Wet IngredientsIn a large bowl, whisk Greek yogurt, eggs, honey, olive oil, and vanilla.
- Step 3: Combine Dry IngredientsIn a separate bowl, stir together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.
- Step 4: Fold and FillAdd dry ingredients to the wet, mixing just until combined. Fold in diced apples. Spoon evenly into muffin tins.
- Step 5: Bake and CoolBake 18–22 minutes or until golden and a toothpick comes out clean. Cool for 5 minutes, then transfer to a rack.
Notes
Secret Tips for Apple Cinnamon Greek Yogurt Muffins
1. Use full-fat Greek yogurt for extra moisture: To make your high-protein muffins rich and tender, opt for full-fat Greek yogurt. It adds creaminess, boosts protein, and keeps these apple cinnamon muffins moist without needing extra oil or butter. 2. Grate the apple finely for better texture: Instead of large chunks, use a fine grater to shred your apple. This lets the apple melt into the batter, keeping each muffin naturally sweet and ultra-moist—perfect for a healthy breakfast muffin that doesn’t taste “healthy.” 3. Don’t overmix the batter: Stir the ingredients just until combined. Overmixing can make your Greek yogurt muffins dense and tough. Gentle folding keeps them light, fluffy, and bakery-style in texture. 4. Add oats or almond flour for fiber and structure: Boost the nutrition and balance the moisture from the apples by folding in a tablespoon of oats or almond flour. It helps bind the muffins and makes them more satisfying for meal prep breakfasts. 5. Sprinkle cinnamon sugar on top before baking: For a golden, slightly crisp muffin top, add a pinch of cinnamon sugar before baking. It brings out the warm spice flavor and gives your apple cinnamon muffins that classic muffin bakery vibe. 6. Store smart for meal prep: These muffins keep best in the fridge in an airtight container lined with paper towels to prevent sogginess. They also freeze well—just reheat for 15 seconds for a warm, protein-packed breakfast on the go. 7. Add protein powder to boost macros: Want to make these apple muffins more filling? Stir in a scoop of unflavored or vanilla protein powder. Just reduce the flour slightly to balance the texture and avoid drying them out.Recipe Overview
- Course: Breakfast, Snack, Meal Prep
- Cuisine: American-Inspired
- Skill Level: Beginner
- Difficulty Level: Easy
- Prep Time: 10 minutes
- Cook Time: 20 minutes
- Total Time: 30 minutes
- Servings: 12 muffins
- Main Ingredients: Greek yogurt, apples, whole wheat flour, cinnamon, eggs
- Best For: On-the-go breakfasts, lunchboxes, post-workout snacks, fall baking cravings
Nutritional Snapshot
| Nutrient | Amount (per muffin) |
|---|---|
| Calories | 142 |
| Protein | 7g |
| Carbohydrates | 19g |
| Fat | 4.5g |
| Fiber | 2g |
| Sugar | 8g |
| Sodium | 150mg |
Budget Breakdown
| Ingredient | Estimated Cost |
| Greek Yogurt | $1.00 |
| Whole Wheat Flour | $0.80 |
| Eggs (2 large) | $0.60 |
| Apples (2 medium) | $1.00 |
| Honey | $0.75 |
| Baking Powder/Soda | $0.20 |
| Cinnamon & Spices | $0.25 |
| Olive Oil | $0.30 |
| Vanilla Extract | $0.40 |
| Total | $5.30 |
| Per Muffin | $0.44 |
Behind the Recipe
I started developing this Apple Cinnamon Greek Yogurt Muffins recipe after realizing that most store-bought muffins are packed with sugar, preservatives, and oils that weigh you down instead of fueling your day. I wanted something that felt bakery-fresh but still nourished my body.
I played around with classic fall flavors like cinnamon, nutmeg, and fresh diced apples, then swapped refined sugar for natural honey and added Greek yogurt for extra protein and moisture. The result? A soft, fluffy, cinnamon-kissed muffin that’s naturally sweet and super satisfying.
I love that these muffins use pantry staples, and they’re incredibly forgiving—meaning you can customize with oats, swap flours, or even add protein powder without compromising texture. These Apple Cinnamon Greek Yogurt Muffins are now a meal prep staple in my home, and I hope they’ll be in yours too.
Why You’ll Love These Apple Cinnamon Greek Yogurt Muffins
A Healthy Muffin That Tastes Like Dessert
Let me tell you—these Apple Cinnamon Greek Yogurt Muffins don’t taste like your typical “healthy muffin.” They’re ultra-moist, perfectly spiced, and naturally sweetened without any refined sugar. The cozy flavor of baked apples mixed with warm cinnamon makes every bite feel like a fall treat straight out of a bakery. But here’s the best part: these muffins are made with wholesome ingredients that fuel your body without sacrificing flavor.
I use unsweetened applesauce and maple syrup to keep things naturally sweet while cutting back on added sugar. The Greek yogurt gives that soft, fluffy crumb we love while boosting protein in every bite. These muffins are great for anyone craving a clean-eating breakfast that still feels indulgent.
If you’re trying to cut back on sugar but love baked goods, this recipe fits the bill—and it’s even better knowing that reducing refined sugars can help regulate blood sugar levels and improve energy, as explained by Harvard Health.
Protein-Packed and Meal Prep Friendly
Each muffin delivers a solid 7 grams of protein, making these a smart choice for a high-protein breakfast or satisfying afternoon snack. The combination of Greek yogurt, eggs, and whole grains gives these muffins long-lasting fuel that keeps me going through my busiest mornings.
I always bake a double batch and stash extras in the freezer—they thaw beautifully in the microwave or toaster oven. Whether you’re eating them on the go or pairing them with a latte, these muffins make weekday breakfasts feel like a win.
Kid-Friendly and Freezer-Ready
These Apple Cinnamon Greek Yogurt Muffins are a hit with my kiddos. They’re soft, lightly sweet, and not overloaded with spice—perfect for young palates. I’ve even packed them in lunchboxes and road trip snack bags with zero complaints (which, if you’re a parent, you know is saying something!).
They freeze exceptionally well, so I recommend baking a dozen and popping a few into a freezer-safe bag. In the morning, just reheat one for 20–30 seconds and you’ve got a warm, protein-rich breakfast ready to go.
Gluten-Friendly Option
While I usually make mine with whole wheat flour for the added fiber and nutrients, you can easily make these muffins gluten-free. Just substitute a 1:1 gluten-free all-purpose baking flour and you’re set. The texture stays soft and tender, and you won’t lose any of that classic muffin fluff.
These muffins are a great way to enjoy baked goods while staying aligned with your wellness goals—low sugar, high protein, and packed with feel-good ingredients that nourish and comfort.
Want More Fall-Inspired Protein Bakes?
Cozy, protein-rich recipes like this one are perfect for cooler mornings and busy weeks. If you’re loving the apple-cinnamon vibes, you’ll definitely want to check out this next one:
Warm Up with This: Exploding Cupcakes with Surprise Candy Center – another fall favorite that packs in protein and comfort in every bite.
Best Shared During
Morning Coffee Breaks
These Apple Cinnamon Greek Yogurt Muffins were practically made for slow mornings and hot mugs. Whether I’m sipping black coffee or something creamier, the warm spice from the cinnamon and sweet-tart apple chunks make each bite feel like comfort in muffin form. They’re a healthier alternative to bakery treats that are often loaded with refined sugars and saturated fats. Pairing protein muffins like these with a source of caffeine may also help stabilize blood sugar and keep mid-morning energy crashes at bay, according to Cleveland Clinic.
On-the-Go Work Snacks
Running out the door? These muffins are the ultimate grab-and-go snack. Thanks to their high-protein content from Greek yogurt and eggs, they keep me full between meetings without making me feel sluggish. I often toss one in my bag with a hard-boiled egg or a banana for a balanced mini meal. Whether you’re meal prepping for work lunches or just need a quick bite between appointments, these muffins make clean eating on busy days super simple.
School Lunches
These Apple Cinnamon Greek Yogurt Muffins are a win with both moms and picky eaters. They’re naturally sweetened with applesauce and maple syrup, totally nut-free, and filled with real fruit—making them perfect for school lunchboxes. I love that they feel like a treat but still sneak in protein and fiber. I bake a batch every Sunday and pack one with lunch for my daughter. They hold up great in a lunchbox and don’t crumble like store-bought muffins.
Weekend Meal Prep
Weekend batch cooking is my love language, and these muffins are one of my go-to meal prep wins. I double the recipe and freeze half so I’m always stocked for the week ahead. They reheat beautifully in the microwave or toaster oven—just 30 seconds for warm, bakery-style muffins you’ll be glad to have on hand. It’s such a time-saver, especially on those chaotic mornings when there’s no time to cook.
Looking for More Muffins That Freeze Like a Dream?
If you love make-ahead breakfast bakes, you’ve got to try this next favorite:
Don’t Miss These: High-Protein Banana Pudding (No-Bake, Meal Prep Friendly, Dairy-Free Option) – naturally sweet, freezer-friendly, and packed with protein for a quick and satisfying snack or breakfast.
Ingredients You’ll Need
- 1 cup plain Greek yogurt (nonfat or full-fat)
- 2 medium apples, peeled and finely diced
- 1 ½ cups whole wheat flour
- 2 large eggs
- ⅓ cup honey or maple syrup
- 2 tbsp olive oil
- 1 tsp baking soda
- ½ tsp baking powder
- 1 ½ tsp cinnamon
- ¼ tsp nutmeg
- 1 tsp vanilla extract
- Pinch of salt
Ingredient Highlights
Greek Yogurt
Provides moisture, a protein boost, and a tender crumb. Use plain unsweetened for best results.
Apples
Go for sweet, crisp varieties like Fuji or Gala. They hold up well and add texture.
Whole Wheat Flour
Adds fiber and nutrients while keeping the muffins hearty.
Cinnamon & Nutmeg
This duo brings out warm fall flavors and balances the natural apple sweetness.
How to Make Apple Cinnamon Greek Yogurt Muffins
Step 1: Preheat and Prep
Preheat oven to 350°F (175°C). Line or grease a muffin tin.
Step 2: Mix Wet Ingredients
In a large bowl, whisk Greek yogurt, eggs, honey, olive oil, and vanilla.
Step 3: Combine Dry Ingredients
In a separate bowl, stir together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.
Step 4: Fold and Fill
Add dry ingredients to the wet, mixing just until combined. Fold in diced apples. Spoon evenly into muffin tins.
Step 5: Bake and Cool
Bake 18–22 minutes or until golden and a toothpick comes out clean. Cool for 5 minutes, then transfer to a rack.
Pro Tips for Success
- Don’t overmix—gentle folding keeps them fluffy.
- Finely dice apples for even distribution and texture.
- Use silicone muffin liners for easy removal.
- Want more sweetness? Add a few mini chocolate chips.
Craving savory instead? Try these High-Protein Lasagna Recipe – Healthy, Macro-Friendly, and Meal Prep Ready
Easy Variations
Apple Oat Greek Yogurt Muffins
If you’re looking to add more fiber and whole grains, swap out ½ cup of the flour for rolled oats. These Apple Oat Greek Yogurt Muffins have a heartier bite and an earthy, nutty undertone that pairs beautifully with the cinnamon and apple. It’s a great option if you’re craving a more wholesome, breakfast-style muffin that feels more like a filling mini-meal. Oats are a natural source of beta-glucan, a fiber that supports heart health and digestion, as noted by Healthline.
Protein Boosted Version
Want to turn these into high-protein apple muffins? Mix in a scoop of your favorite vanilla whey or plant-based protein powder and slightly reduce the flour to balance the texture. I usually take out about 2–3 tablespoons of flour when I add protein powder. This turns an already protein-rich muffin into a post-workout powerhouse with even more staying power.
Apple Carrot Muffins
Looking for a way to sneak in extra veggies for your kids (or yourself)? Fold in ½ cup of grated carrot along with the apple. The carrots blend in seamlessly, adding natural sweetness, moisture, and an extra punch of vitamin A and fiber. It’s like a hybrid between carrot cake and apple muffins—and it’s 100% lunchbox approved.
Gluten-Free Apple Cinnamon Muffins
To make gluten-free apple cinnamon Greek yogurt muffins, all you need is a 1:1 gluten-free all-purpose baking flour. I’ve had great results using blends that include rice flour, potato starch, and xanthan gum. Just keep an eye on the baking time—gluten-free muffins may need an extra 1–2 minutes depending on the brand you use. The flavor stays the same, and you’ll still get that soft, tender crumb.
Craving More Protein Muffins That Actually Taste Good?
If you love muffins that don’t compromise flavor for nutrition, here’s another one you’ll want to bake on repeat:
Don’t Miss This Protein Favorite: Honey Peach White Cheddar Grilled Cheese – they’re freezer-friendly, moist, and packed with clean protein to fuel your morning routine.
Storage & Reheat Tips
- Store in an airtight container at room temp for 2–3 days.
- Refrigerate up to 1 week.
- Freeze individually wrapped muffins for up to 3 months.
- Reheat in the microwave for 15–20 seconds or thaw overnight.
Frequently Asked Questions
Are Greek yogurt muffins healthy?
Yes! These apple cinnamon Greek yogurt muffins are high in protein and low in added sugar, making them a nutrient-dense breakfast or snack. Thanks to the Greek yogurt, they provide gut-friendly probiotics and a creamy texture without needing lots of oil. According to Healthline, Greek yogurt is linked to better digestion, bone health, and increased satiety.
Can I make apple cinnamon muffins without oil?
Definitely. You can leave out the oil and increase the amount of Greek yogurt slightly to keep moisture in balance. Keep in mind that the muffins may be slightly denser but still delicious. It’s a great trick for anyone looking for a low-fat muffin recipe with Greek yogurt.
What type of apple is best for baking muffins?
Gala, Fuji, and Honeycrisp are my go-to apples for baking. They’re naturally sweet, hold their shape well, and don’t overpower the cinnamon. If you’re aiming for a bit more tartness, Granny Smith works beautifully too.
Can I make these muffins dairy-free?
Yes! For dairy-free apple muffins with yogurt, simply use a plant-based yogurt alternative—like coconut or almond milk yogurt—and make sure the rest of your ingredients (like protein powder, if used) are also dairy-free. I like using maple syrup instead of honey to keep them fully plant-based.
How do I increase protein in Greek yogurt muffins?
To make high-protein apple cinnamon Greek yogurt muffins, just add a scoop of vanilla or unflavored protein powder to the batter and slightly reduce the flour (about 2–3 tablespoons). This keeps the texture balanced and adds 5–10 grams of extra protein per muffin depending on the powder used.
Are these muffins low sugar?
Yes, these are low-sugar apple cinnamon muffins sweetened naturally with honey or maple syrup. There’s no refined sugar involved, and the apples add a nice natural sweetness on their own. That’s what makes them great for meal prep and even kid-friendly snacks.
Can I add oats to this muffin recipe?
Absolutely. Subbing in ½ cup of rolled oats for flour adds heartiness, fiber, and a slightly nutty flavor. It turns the texture into something closer to apple oat protein muffins—perfect for a more filling bite.
Do I need to peel the apples?
That’s up to you. Leaving the skins on adds more fiber and a little texture, while peeling creates a smoother, bakery-style muffin. I personally leave the peels on when I’m making these for myself, and peel them when I bake for picky eaters.
Can I freeze apple cinnamon Greek yogurt muffins?
Yes—these muffins freeze wonderfully. Just let them cool completely, then store them in a freezer-safe bag or container. Reheat in the microwave or toaster oven for a quick meal prep muffin that’s ready in seconds. This makes them perfect for batch baking and busy mornings.
What flour can I use to make these gluten-free?
To make gluten-free Greek yogurt muffins, simply use a 1:1 gluten-free all-purpose flour blend that contains xanthan gum. I’ve tested this recipe with a few popular brands, and the results are still moist and fluffy with no compromise on flavor. You can read more about gluten-free flour alternatives from Cleveland Clinic.
Can I make these apple muffins refined sugar free?
Yes, these muffins already use natural sweeteners like honey or maple syrup instead of refined white sugar. You can also use mashed banana or unsweetened applesauce to sweeten them up naturally if you’re trying to avoid all forms of added sugar.
Final Thoughts
These Apple Cinnamon Greek Yogurt Muffins are a must-bake for anyone who wants simple, nourishing recipes that taste just like a bakery treat. I love how they come together with ingredients I always have on hand, and they never fail to make my kitchen smell incredible. Whether you’re baking for your kids, for your meal prep lineup, or just for yourself (hello, solo coffee and muffin moment), this recipe has your back.
If you’re on the lookout for easy, high-protein muffin recipes with real ingredients and real flavor, this one deserves a spot in your rotation. Sweet apples, cozy cinnamon, and creamy Greek yogurt make a muffin that satisfies without the sugar crash.
Go ahead—bake a batch, share with someone you love, and keep a few in the freezer for those mornings when you just need a little something warm and sweet to start the day right.
“Warm cinnamon, juicy apples, and tender protein-rich muffins—this is the kind of comfort food that makes meal prep feel like a treat.” – Sam
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Moist, high-protein muffins made with real apples, cozy cinnamon, and creamy Greek yogurt—perfect for healthy breakfast meal prep and snack cravings alike.
