If you’re craving a cozy, comforting treat that feels like a hug from the inside, look no further than this Whole30 Cinnamon Apple Muffins Recipe. Bursting with tender apples and a swirl of warm cinnamon, these muffins strike the perfect balance between moist and fluffy with just the right touch of sweetness. They’re ideal for breakfast, an afternoon snack, or even a wholesome dessert. What makes this recipe truly stand out is how it marries simple pantry essentials with fresh fruit and a hint of spice, making every bite a delight. Let me take you through everything you need to know to whip up these irresistible muffins that taste like fall in every mouthful.

Ingredients You’ll Need
Gathering your ingredients is the first step toward muffin magic. Each one plays a crucial role, from giving structure to delivering flavor and texture, ensuring your Whole30 Cinnamon Apple Muffins Recipe turns out just right every time.
- 2 cups (240 g) all‑purpose flour: Provides the perfect structure for tender yet sturdy muffins.
- 1 ½ teaspoons baking powder: Helps your muffins rise beautifully and become delightfully fluffy.
- ½ teaspoon baking soda: Adds a little boost to the leavening process for an ideal crumb.
- 2 teaspoons ground cinnamon: Infuses the batter with that signature warm spice that makes these muffins unforgettable.
- ½ teaspoon fine sea salt: Balances the sweetness and elevates all the flavors.
- 1 ½ cups (180 g) peeled & diced Honeycrisp or Granny Smith apple: Brings juicy bursts of fresh apple flavor and natural sweetness.
- 1 Tablespoon all‑purpose flour (to coat apples): Prevents the apples from sinking and keeps every bite juicy.
- ½ teaspoon ground cinnamon (to coat apples): Adds a subtle spice to each apple piece for extra depth.
- ½ cup (113 g) unsalted butter, softened: Creates rich, moist crumb and buttery goodness.
- ½ cup (100 g) packed light brown sugar: Adds caramel notes and tender texture.
- ½ cup (100 g) granulated sugar: Provides sweetness and helps with a soft crumb.
- 2 large eggs, room temperature: Binds ingredients and contributes fluffiness.
- 2 teaspoons pure vanilla extract: Enhances the warm flavors and adds a lovely aroma.
- ½ cup (120 g) plain Greek yogurt or sour cream: Keeps the muffins moist and adds a slight tang.
- ¼ cup (60 ml) milk or buttermilk (2–3 %): Lightens the batter for a tender crumb.
- ¾ cup (90 g) all‑purpose flour (for streusel): Creates the crumbly topping that adds texture.
- â…“ cup (65 g) packed brown sugar (for streusel): Sweetens the crunchy topping with deep molasses notes.
- 1 teaspoon ground cinnamon (for streusel): Adds that unmistakable cinnamon flair to the topping.
- 4 Tablespoons (56 g) melted unsalted butter (for streusel): Binds the streusel and adds richness.
How to Make Whole30 Cinnamon Apple Muffins Recipe
Step 1: Preheat and Prepare Your Muffin Tin
Start by setting your oven to 425 °F (218 °C). Line a 12-cup muffin tin with liners and lightly grease them so your muffins won’t stick and will pop out easily after baking. This simple prep sets the stage for muffin perfection.
Step 2: Make the Optional Streusel Topping
If you like a crunchy, sweet topping, mix ¾ cup flour, ⅓ cup brown sugar, and 1 teaspoon cinnamon in a bowl. Drizzle 4 tablespoons melted butter over the mixture and stir until clumps form. Pop this into the fridge to chill; it’ll give your muffins that irresistible crumble while you prepare the batter.
Step 3: Toss the Apples
Coat the peeled and diced apples with 1 tablespoon flour and ½ teaspoon cinnamon. This little trick ensures the apples won’t sink to the bottom of the muffins and spreads their warm cinnamon flavor evenly throughout every bite.
Step 4: Mix the Dry Ingredients
In a separate bowl, whisk together the flour, baking powder, baking soda, cinnamon, and salt. Mixing these dry components well will guarantee that your muffins rise evenly and have consistent flavor in each morsel.
Step 5: Cream the Butter and Sugars
Using a large bowl, beat together the softened butter, brown sugar, and granulated sugar until pale and fluffy—about two minutes. This step is vital because it creates air pockets in the batter, contributing to beautifully light muffins.
Step 6: Add Eggs and Vanilla
Beat in the eggs one at a time to ensure full incorporation, then stir in the vanilla extract. These add richness and depth, making your muffins fragrant and full of flavor.
Step 7: Stir in Yogurt and Milk
Mix in the Greek yogurt or sour cream and milk. Don’t worry if the batter looks a bit curdled—this is normal and signals moist, tender muffins ahead.
Step 8: Combine Wet and Dry Ingredients
Fold the dry ingredients into the wet mixture just until no flour streaks remain. Avoid overmixing here to keep the batter thick and your muffin tops domed and inviting.
Step 9: Fold in the Cinnamon-Coated Apples
Gently stir the apple pieces into the batter, distributing them evenly without smashing. This ensures juicy pockets of apple in every bite.
Step 10: Fill Muffin Cups and Add Streusel
Divide batter evenly into the prepared muffin cups, filling them all the way to the top for tall, fluffy muffins. If you made the streusel topping, sprinkle it generously over each muffin now.
Step 11: Bake with Temperature Adjustments
Bake your muffins at the initial high temperature of 425 °F for 5 minutes—this jump-starts a lovely rise and creates beautiful tops. Then, without opening the oven door, reduce the heat to 350 °F (177 °C) and bake for an additional 15 to 17 minutes, or until a toothpick comes out clean.
Step 12: Cool and Enjoy
Let the muffins rest in the pan for 5 minutes before transferring them to a wire rack to cool. While warm, you can brush the tops with melted butter and dust with cinnamon sugar for an extra touch of irresistible flair. Then, inhale that cinnamon-apple aroma and savor your creation!
How to Serve Whole30 Cinnamon Apple Muffins Recipe

Garnishes
Sprinkling a light dusting of cinnamon sugar or adding a drizzle of honey glaze instantly elevates these muffins. A pat of softened butter melts beautifully on warm muffins, enhancing every bite.
Side Dishes
Pair your muffins with a cup of hot coffee or chai tea for a cozy snack, or serve alongside fresh fruit and yogurt for a balanced breakfast plate that’s as comforting as it is nourishing.
Creative Ways to Present
Try slicing the muffins in half and spreading almond or cashew butter inside for a protein boost, or stack them up on a brunch table as part of a seasonal spread complete with homemade jam and nuts for added texture and flavor.
Make Ahead and Storage
Storing Leftovers
Store leftover muffins in an airtight container at room temperature for up to 3 days. This keeps them soft and moist while preserving their fresh-baked aroma.
Freezing
Wrap each muffin individually in plastic wrap or foil and place in a freezer-safe bag. They can be frozen for up to 3 months without losing their delicious flavor or texture, making them perfect for busy mornings.
Reheating
To enjoy your muffins warm after storage, simply microwave them for about 20 seconds or warm them in a 350 °F oven for 5 to 7 minutes. This revives that freshly baked taste and texture effortlessly.
FAQs
Can I use a different type of apple for this Whole30 Cinnamon Apple Muffins Recipe?
Absolutely! While Honeycrisp and Granny Smith are recommended for their tartness and firmness, you can substitute with any firm apples you have on hand. Just keep in mind sweeter varieties may alter the overall sweetness.
Is it possible to make these muffins dairy-free?
Yes, you can swap the butter for a dairy-free alternative like coconut oil and use a plant-based yogurt to keep the moisture intact without compromising flavor or texture.
How do I know when the muffins are fully baked?
The best indicator is a toothpick inserted in the center coming out clean or with just a few moist crumbs. The muffins should also be golden brown on top and spring back lightly when touched.
Can I prepare the batter the night before?
It’s best to bake the muffins fresh for optimal texture, but you can prepare the batter the night before and refrigerate it covered. Give it a gentle stir before filling your muffin tins and baking.
Can this Whole30 Cinnamon Apple Muffins Recipe be made gluten-free?
Yes! You can substitute the all-purpose flour with a gluten-free baking flour blend that measures cup-for-cup. Make sure the blend contains xanthan gum or another binder to maintain texture.
Final Thoughts
This Whole30 Cinnamon Apple Muffins Recipe is a heartwarming and versatile treat that fits perfectly into your daily routine, whether you’re fueling a busy day or simply craving something comforting. The way the cinnamon and apple come together with a tender crumb is truly something special, and I can’t wait for you to try them out. Once you do, I’m sure these muffins will become a beloved staple that everyone looks forward to, creating a little warmth and sweetness with every bite.
Print
Whole30 Cinnamon Apple Muffins Recipe
- Prep Time: 10 minutes
- Cook Time: 25 minutes
- Total Time: 35 minutes
- Yield: 12 muffins
- Category: Breakfast, Snack, Dessert
- Method: Baking
- Cuisine: American
Description
These Whole30 Cinnamon Apple Muffins are a delicious and wholesome treat featuring tender apple pieces coated in cinnamon and baked into moist, fluffy muffins. Topped optionally with a spiced streusel, these muffins are perfect for breakfast or a snack, combining warm spices with the sweet tang of apples for a comforting bite.
Ingredients
Dry Ingredients
- 2 cups (240 g) all‑purpose flour
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- 2 teaspoons ground cinnamon
- ½ teaspoon fine sea salt
Apple Coating
- 1 ½ cups (180 g) peeled & diced Honeycrisp or Granny Smith apple
- 1 Tablespoon all‑purpose flour (to coat apples)
- ½ teaspoon ground cinnamon (to coat apples)
Wet Ingredients
- ½ cup (113 g) unsalted butter, softened
- ½ cup (100 g) packed light brown sugar
- ½ cup (100 g) granulated sugar
- 2 large eggs, room temperature
- 2 teaspoons pure vanilla extract
- ½ cup (120 g) plain Greek yogurt or sour cream
- ¼ cup (60 ml) milk or buttermilk (2–3 %)
Streusel Topping (Optional)
- ¾ cup (90 g) all‑purpose flour
- â…“ cup (65 g) packed brown sugar
- 1 teaspoon ground cinnamon
- 4 Tablespoons (56 g) melted unsalted butter
Instructions
- Preheat & prep: Set your oven to 425 °F (218 °C). Line a 12‑cup muffin tin with liners and lightly grease them to prevent sticking.
- Prepare the optional streusel: In a small bowl, mix together ¾ cup flour, ⅓ cup brown sugar, and 1 teaspoon cinnamon. Drizzle in 4 tablespoons melted butter and stir until clumps form. Chill this mixture while you prepare the batter.
- Prepare the apples: Toss the diced apples with 1 tablespoon flour and ½ teaspoon cinnamon. This coating helps prevent the apples from sinking to the bottom of the muffins during baking.
- Mix dry ingredients: In a separate bowl, whisk together 2 cups flour, 1 ½ teaspoons baking powder, ½ teaspoon baking soda, 2 teaspoons cinnamon, and ½ teaspoon salt.
- Cream butter and sugars: In a large bowl, beat ½ cup softened butter with ½ cup light brown sugar and ½ cup granulated sugar until the mixture is pale and fluffy, about 2 minutes.
- Add eggs and vanilla: Beat in the eggs one at a time, ensuring each is fully incorporated before adding the next. Then add 2 teaspoons vanilla extract and mix well.
- Incorporate dairy: Mix in ½ cup Greek yogurt (or sour cream) and ¼ cup milk. The batter may appear a bit curdled at this point—that’s normal.
- Combine wet and dry ingredients: Fold the dry ingredients into the wet mixture gently, mixing just until no flour streaks remain. The batter will be thick, which helps produce tall, domed muffins.
- Fold in apples: Gently stir in the cinnamon-coated apple pieces, ensuring even distribution without overmixing.
- Fill muffin cups and add streusel: Divide the batter evenly among the muffin cups, filling each to the brim. If using, sprinkle the chilled streusel topping over each muffin.
- Bake in two stages: Bake the muffins for 5 minutes at 425 °F. Without opening the oven door, reduce the temperature to 350 °F (177 °C) and bake for an additional 15 to 17 minutes, or until a toothpick inserted in the center comes out clean.
- Cool and serve: Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack to cool completely. Optionally, brush the warm tops with melted butter and dust with cinnamon sugar for an extra special finish.
Notes
- Using tart apples like Granny Smith or Honeycrisp balances the sweetness and adds a fresh flavor.
- Coating apples in flour and cinnamon helps prevent them sinking and keeps the muffins tender.
- The two-stage baking method helps create tall muffins with nicely domed tops.
- The optional streusel provides a delightful crunchy cinnamon-sugar topping.
- Ensure all wet ingredients are at room temperature for better mixing and texture.
- You can substitute the Greek yogurt with sour cream for a slightly different tang.
- Store muffins in an airtight container at room temperature for up to 3 days or freeze for longer storage.