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Healthy Apple Pumpkin Muffins

These soft and fluffy Apple Pumpkin Muffins are the grab-and-go breakfast you need this fall! Flavored with pumpkin pie spice and topped with crunchy toasted pecans, you won’t find a more festive dish.

Easy Apple Pumpkin Muffins with Pecans

There’s a never-ending debate over which fall flavor is better – apple or pumpkin. I say we should appreciate them equally! These moist and tender apple pumpkin muffins give you the best of both worlds, all wrapped up into a healthy breakfast.

Not only is this a gluten-free recipe, but it’s also dairy-free and refined sugar free. The muffins use coconut oil instead of butter and maple syrup in place of granulated sugar. Trust me, you won’t taste the difference!

In addition to providing flavor, the pumpkin puree and applesauce keep these muffins extra moist. And the use of both baking powder and baking soda ensure they’ll be extra fluffy. Once you add the fresh chunks of apple and the chopped pecans, your muffins are destined for deliciousness. You’re going to FALL in love!

Apple pumpkin muffins scattered across a kitchen counter alongside a glass of milk and a bowl of pumpkin puree

Recipe Ingredients

Even though these muffins are loaded with pumpkin puree, diced apples and more, they keep a pretty low profile when it comes to ingredients. Here’s what you’ll need:

  • Gluten Free 1:1 Baking Flour: Feel free to use regular baking flour if your diet permits.
  • Maple Syrup: Make sure you’re using pure maple syrup instead of maple flavored corn syrup.
  • Pumpkin Pie Spice: You can’t have the ultimate fall breakfast without some pumpkin spice!
  • Baking Powder & Baking Soda: You’ll need both in order for your muffins to come out extra fluffy.
  • Salt: To keep the muffins nice and moist.
  • Pumpkin Puree: Canned or homemade. If you use homemade puree, be sure to drain out as much moisture as you can.
  • Vanilla Extract: This sets the stage so all the other flavors can shine!
  • Applesauce: Unsweetened.
  • Coconut Oil: Melted.
  • Eggs: You’ll need two eggs to help bind all the ingredients together.
  • Granny Smith Apple: Peeled and diced.
  • Chopped Pecans: Optional, for a crunchy nut topping.

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A bowl of diced apples, two eggs, applesauce and the rest of the ingredients on top of a marble counter

What Apples are Best for Muffins?

In general, you want to use a firmer type of apple when you’re making muffins. That way, they will hold their shape and won’t get mushy when baked. For these muffins in particular, I like to use Granny Smith apples – they have a wonderfully tart flavor that compliments the sweetness of the pumpkin perfectly.

Don’t have Granny Smith apples on hand? There are plenty of other tart and crisp varieties that also work well in this recipe. McIntosh, Pink Lady, Braeburn and Jonathan are just a few examples.

A white cutting board holding freshly baked apple pumpkin muffins with chopped pecans on top

How to Make Apple Pumpkin Muffins

Preparing these muffins is no problem for even the most inexperienced bakers. They only take about 30 minutes!

Heat Oven: Preheat the oven to 350°F

Combine Dry Ingredients: Add the gluten-free flour, pumpkin pie spice, baking powder, baking soda and salt to a large bowl. Mix until combined.

Combine Wet Ingredients: Add the pumpkin puree, unsweetened applesauce (make your own by using my Instant Pot Unsweetened Applesauce Recipe), coconut oil, vanilla extract and eggs to another small bowl.

Combine Wet & Dry Ingredients: Pour the wet ingredients over the dry ingredients and mix thoroughly.

The combined wet ingredients being poured into the bowl of dry ingredients

Add Apples: Fold in the diced granny smith apples.

The nearly-completed batter in a glass mixing bowl with diced Granny Smith apples on top

Pour into Muffin Tin & Top with Pecans: Place a cupcake liner into each muffin tin. Fill each muffin tin about 3/4 of the way full with batter. Top with chopped pecans, if desired.

Bake: Bake the muffins for 20-24 minutes, until a toothpick inserted into the center comes out clean.

Let Sit: Remove your muffins from the oven and let them sit for 5-10 minutes before enjoying.

An overhead shot of a twelve-count cupcake tin filled with baked muffins

Tips for Success

There’s no need for trial and error when it comes to these pumpkin muffins. I have all the advice you need to get them just right!

  • Use a Ripe Apple: Not sure how to tell whether your apple is ripe, underripe or overripe? It should be firm with no large bruises or discoloration and the stem should come off easily when twisted and pulled.
  • Peel the Apple: The baking process can cause the skin of your apple to separate from the inside. For this reason, I recommend peeling your apple before you dice it up.
  • Use High-Quality Cupcake Liners: I strongly suggest using cupcake liners with a nonstick coating. If you can’t find those, simply grease the cupcake liners with a little cooking spray. Otherwise, the muffins will stick when you try to remove the liners.
  • Toast the Nuts! If you want to get the best flavor out of your pecans, toast them in the oven before adding them to your muffins. It’s a small step, and the amount of flavor it adds is totally worth it.
Two halves of an apple muffin on a white plate with more muffins beside it

Serving Suggestions

If you’re serving your apple pumpkin muffins for a big fall brunch, then you probably want some other festive dishes to go along with them. I’m full of irresistible ideas!

  • Pair with Breakfast Potatoes: Roasted potatoes are a great dish for any holiday season. These Easy Breakfast Potatoes with peppers and onions will take your brunch to the next level! I love serving them with sautéed turkey sausage in the fall.
  • Serve with Butternut Squash: Butternut squash is a pumpkin-like gourd that’s typically enjoyed around the holidays. You can prepare it in tons of different ways, but one of my favorites is this Creamy Bacon Butternut Squash Soup! It’s the perfect cozy soup to enjoy on a cool fall morning.
  • Pair with a Breakfast Bowl: If you’re not gluten-free, I highly recommend serving your muffins as a side dish for these Harvest Roasted Vegetable Grain Bowls! They’re filled with fluffy farro, hearty veggies and plenty of seasonings, then topped with an over easy egg.
Three homemade muffins inside a muffin tin next to a striped kitchen towel

How to Store and Warm Muffins

Once cooled, these muffins can be stored in the fridge for up to 5 days. They should be kept in an airtight container. You can bring them to room temperature before serving them or warm each muffin in the microwave for 10-15 seconds at a time.

Can I Freeze These?

Yes, you can. Yay meal prep! To freeze your muffins, simply wrap each cooled muffin in plastic wrap or heavy-duty aluminum foil. Alternatively, you can seal them in a freezer bag with all the air squeezed out. Enjoy your frozen muffins within 3 months, thawing them out in the fridge overnight before digging in.

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Two apple pecan muffins stacked on top of one another with a glass of milk behind them

Healthy Apple Pumpkin Muffins

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  • Author: Krista
  • Prep Time: 10 minutes
  • Cook Time: 24 minutes
  • Total Time: 34 minutes
  • Yield: 12 1x
  • Category: Breakfast
  • Method: Oven
  • Cuisine: American
  • Diet: Gluten Free


These soft and fluffy Apple Pumpkin Muffins are the grab-and-go breakfast you need this fall! Flavored with pumpkin pie spice and topped with crunchy toasted pecans, you won’t find a more festive dish.


  • 2 cups of Gluten Free 1:1 Baking Flour
  • 1/2 cup maple syrup
  • 1 1/4 teaspoon pumpkin pie spice
  • 3/4 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 3/4 cup pumpkin puree
  • 1 teaspoon vanilla extract
  • 1/2 cup of unsweetened apple sauce
  • 1/4 cup coconut oil, melted
  • 2 eggs
  • 1/2 cup of diced granny smith apple, peeled
  • chopped pecans for topping {optional}


  1. Preheat oven to 350°F.
  2. In a large bowl, mix gluten free flour, pumpkin pie spice, baking powder, baking soda, and salt. Mix until combined.
  3. To another small bowl, add pumpkin puree, unsweetened apple sauce, coconut oil, vanilla extract and eggs.
  4. Pour wet ingredients over dry ingredients and mix thoroughly.
  5. Fold in diced granny smith apples.
  6. Place cupcake liners in each muffin tin. Fill each muffin tin about 3/4 full with apple pumpkin mixture. Top with chopped pecans (optional).
  7. Bake for 20-24 minutes. Until toothpick comes out clean when inserted into muffin.
  8. Remove from oven and let sit for 5-10 minutes.


  • Serving Size: 1 muffin
  • Calories: 184
  • Sugar: 10 g
  • Sodium: 185 mg
  • Fat: 5 g
  • Saturated Fat: 4 g
  • Carbohydrates: 31 g
  • Fiber: 1 g
  • Protein: 3 g
  • Cholesterol: 31 mg

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