Healthy Apple Cinnamon Muffins

These healthy apple cinnamon muffins are naturally sweetened with maple syrup and packed with fresh shredded apples and warm cinnamon spices. I started making this recipe when I needed a breakfast option that felt like a treat but didn’t leave me crashing an hour later.

The combination of whole wheat flour and Greek yogurt keeps them moist and tender, while the coconut oil adds just the right amount of richness. They’re my go-to during fall mornings when there’s a chill in the air and you need something comforting to pair with your coffee.

Ingredients You’ll Need

• 1 3/4 cups whole wheat pastry flour
• 1 teaspoon baking soda
• 2 teaspoons cinnamon
• 1/2 teaspoon salt
• 2 large eggs, room temperature
• 1/2 cup pure maple syrup
• 1/2 cup plain Greek yogurt, room temperature
• 1/3 cup almond milk (or milk of choice)
• 3 tablespoons coconut oil, melted and cooled
• 1 1/2 teaspoons vanilla extract
• 1 cup shredded apple (about 1 medium apple, peeled)

How To Make Apple Cinnamon Muffins

1. Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or grease wells with cooking spray.
2. Whisk together the whole wheat pastry flour, baking soda, cinnamon, and salt in a large mixing bowl until evenly combined.
3. Beat the eggs in a separate medium bowl, then add maple syrup, Greek yogurt, almond milk, melted coconut oil, and vanilla extract, whisking until smooth.
4. Pour the wet ingredients into the dry ingredients and gently fold together using a spatula until just combined, don’t overmix or muffins will be dense.
5. Fold in the shredded apple, distributing it evenly throughout the batter with gentle strokes.
6. Divide the batter evenly among the prepared muffin cups, filling each about 3/4 full.
7. Bake for 18-22 minutes until the tops are golden brown and a toothpick inserted into the center comes out clean or with just a few moist crumbs.
8. Cool in the pan for 5 minutes, then transfer muffins to a wire rack to cool completely.

Why You’ll Love This Recipe

These muffins strike that perfect balance between wholesome and indulgent. The whole wheat pastry flour gives them a lighter texture than regular whole wheat while still providing fiber and nutrients. Greek yogurt adds protein and creates an incredibly moist crumb that stays fresh for days. Plus, using maple syrup instead of refined sugar means you’re getting trace minerals and a more complex sweetness that complements the apple and cinnamon beautifully.

The shredded apple pieces throughout create little pockets of moisture and natural sweetness. As the muffins bake, the apples soften and almost caramelize slightly, creating these wonderful tender bits. You can taste the apple in every bite, not just see it.

Best Apples for Baking Muffins

Choosing the right apple makes a difference in texture and flavor. Granny Smith apples add a nice tartness that balances the maple syrup’s sweetness and hold their shape well during baking. Honeycrisp apples provide natural sweetness and stay fairly firm. Gala or Fuji apples work too if you prefer a sweeter, softer result.

I usually peel the apples before shredding, but you can leave the peel on if you want extra fiber and don’t mind flecks of color in your muffins. Just make sure to shred them right before mixing, if they sit too long, they’ll oxidize and turn brown.

Storage and Make-Ahead Tips

Store these healthy apple cinnamon muffins in an airtight container at room temperature for up to 3 days or in the refrigerator for up to a week. The fridge actually helps them stay moist longer. You can also freeze them for up to 3 months, just wrap individually in plastic wrap, then place in a freezer bag. Thaw overnight in the fridge or pop a frozen muffin in the microwave for 30-45 seconds.

These muffins are fantastic for meal prep. I often make a double batch on Sunday and keep them in the fridge for quick breakfasts all week. They’re also great for lunchboxes or afternoon snacks. Try pairing them with similar wholesome treats like Lemon Poppyseed Zucchini Muffins for variety throughout the week.

Customization Ideas

Feel free to add 1/2 cup of chopped walnuts or pecans for extra crunch and healthy fats. You can also stir in 1/4 cup of raisins or dried cranberries if you want more sweetness and texture. For a spice variation, add 1/4 teaspoon of nutmeg or a pinch of ground ginger alongside the cinnamon.

If you’re not a fan of maple syrup, honey works as a substitute, though it’ll make the muffins slightly sweeter and less complex in flavor. Regular milk can replace almond milk, and butter works instead of coconut oil, just melt it and let it cool before adding.

Notes

• Don’t skip letting the coconut oil cool before adding it to the wet ingredients, or it might scramble the eggs.
• The batter will be fairly thick, which is normal, this creates those nice domed muffin tops.
• For extra tender muffins, let the batter rest for 5 minutes before filling the muffin cups.
• If your muffins brown too quickly on top, tent them with foil during the last 5 minutes of baking.
• Room temperature eggs and yogurt mix more easily and create a better texture.
• You can make mini muffins instead, just reduce baking time to 12-15 minutes.

Frequently Asked Questions

Can I use all-purpose flour instead of whole wheat pastry flour?
Yes, you can substitute all-purpose flour in equal amounts. The muffins will be lighter in color and texture but won’t have quite as much fiber or that subtle nutty flavor from the whole wheat.

Why did my muffins turn out dense?
The most common reason is overmixing the batter after combining wet and dry ingredients. Mix just until you don’t see dry flour anymore, some small lumps are fine. Also make sure your baking soda is fresh and not expired.

Can I reduce the sugar in this recipe?
You can reduce the maple syrup to 1/3 cup if you prefer less sweetness, especially if using sweeter apples. The muffins will be a bit less moist but still good. I wouldn’t go lower than that or the texture suffers.

How do I keep the apples from sinking to the bottom?
Make sure you’re using shredded apple rather than chunks, and that your batter is thick enough. Tossing the shredded apple in a teaspoon of flour before folding it in can also help.

Can I make these vegan?
Yes, replace the eggs with flax eggs (2 tablespoons ground flaxseed mixed with 6 tablespoons water, let sit 5 minutes), and use dairy-free yogurt. The texture will be slightly different but still delicious.

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