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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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54 comments on “Healthy Apple Pumpkin Muffins”

  1. I am going to be making these muffins for sure. Now I have another recipe for the apples and pumpkins we grow 🙂 I could use some recipes for pears now! We have a fruit orchard and I can always use more ideas besides just canning them. Thanks for the recipe 🙂

    1. Awesome Anne. How fun that you have a fruit orchard! I would love that! I hope you enjoy the muffins!

      I will get on trying to think of pear recipes for you to use. 🙂 Thanks for stopping by.

  2. I just made these last night and they’re delicious! I love the apple and pumpkin together! I had enough pumpkin puree & diced apples from two apples from the can to make 2 batches! You can prolly add that 1 apple is enough to get 1/2 cup diced apples. I didn’t know so I diced two. I paired the muffins with pumpkin butter from Trader Joe’s and it’s perfect! Thanks so much for the recipe! Also, my muffins didn’t stick too much to the liners, at least not more than what I would expect from other muffins.

    1. OH… the pumpkin butter sounds delicious! Great tip Alena! Thank you so much. Can’t wait to try it with that… the more pumpkin the better. 🙂 I will change the recipe to say 1 apple just in case people are wondering. 🙂 I’m so glad you liked them and that they didn’t stick too bad to the liner for you. Thanks for stopping by and letting me know, I so appreciate it! {and it definitely made my day}

  3. Quick question! I’m hoping to make these very soon (as in this afternoon 😉 ), but I do not have any greek yogurt in the house. I do have traditional vanilla yogurt and sour cream. Would one of those work well as a substitute? Thank you SO much! I can’t wait to try one of these little pieces of Fall!

    1. Absolutely, I would use the traditional vanilla yogurt. Be sure to spray the pan with PAM before you put the cupcake liners in. These tend to stick to the liner a bit, but they are absolutely delicious! 🙂

  4. Your muffins look amazing! Thanks for linking up with me for Friday Favorites. I’m featuring you this week.

  5. Avatar photo
    Laura @ The Rookie Cook

    Yummy, these look so good! I love the combo of pumpkin and apple – my two favorites lately! Pinned!

  6. Hi Krista! Stopping by from Show Stopper Saturday and had to check out these amazing looking muffins. Can’t wait to make these. Pinning!

    1. Thanks so much Erin! I hope you love them as much as we did! Thanks for the “pin love”. 🙂 Hope you have a great weekend!

    1. Thanks so much Lisa, they were delicious especially with the pecan toppings. The crate is definitely becoming one of my favorites. 🙂

  7. Avatar photo
    Pamela @ Brooklyn Farm Girl

    Apple and pumpkin? These are sweet words to my ears! Can’t wait to make these after we go apple picking soon!

    1. Oh gosh! Jealous, I wish we had apple orchards in Texas. Apparently they don’t grow well here.. too stinking hot! Major boos on that. YEAH for apple and pumpkin season. 🙂

  8. Avatar photo
    Lynn H @ Turnips 2 Tangerines

    Wow, your muffins look delicious! Perfect for this time of year~Lynn @ Turnips 2 Tangerines

  9. wow! Those look perfect… love the nuts on top and your photos are gorgeous too! Finally getting around to view all the other fall links…. fun roundup! Emily

    1. Yeah, this roundup there were definitely some awesome yummy meals. I think I pinned everything because they all looked wonderful! Thanks for stopping by Emily and the sweet comments! 🙂

  10. These look really good and I love the pecans on top. I LOVE the photo with muffins in the old crate!! Very good styling!!

    1. Thanks Paula. I actually keep my olive oil, vinegar, salt & such in that crate. I was trying to find something to put the muffins in and saw that out of the corner of my eye. 🙂 Viola! Thanks for the sweet comments!

  11. Avatar photo
    Tina @ Tina's Chic Corner

    Seriously pumpkin stuff is all over pinterest! I’ve got a long list of what I want to make…wonder how many I’ll actually get to. 😉 Loving these muffins! Your pictures are amazing. 🙂

    1. hahaah.. for real! Its like a pumpkin party. I’m ok with that though because pumpkins are my favorite thing about the fall. 🙂 Thanks the encouragement on the pictures, means alot Tina! 🙂

  12. Avatar photo
    Jamie @lifelovelemons

    Love the huge chunks of pecan on top of these! Fall has definitely arrived and I love it!

    1. Thanks Jamie! The crunch of the pecans was a great addition to these muffins. Yeah for fall! 🙂 My favorite time of the year.

  13. Avatar photo
    Anne ~ Uni Homemaker

    These muffins totally scream autumn –pumpkin and apple together? How clever! Will definitely be putting this on my to-bake list. Pinning! Have a great week Krista. 🙂

    1. Yeah for autumn, love when I can start making the pumpkin and apple recipes! 🙂 I hope you like it just as much as we did Anne! Have a great week and thanks for stopping by.

  14. I always think of apple and pumpkin as separate fall flavors….why have I never thought of combining them before? These muffins sound fabulous!

    1. Thanks Danelle, you’ve shown me the “light” food wise a couple of times too girl with all your delicious recipes! 🙂 Now, go make some apple pumpkin muffins! hehe..

  15. Avatar photo

    These look fantastic, Krista! I love the idea of combining two of my favorite fall ingredients into one yummy, healthy muffin! Pinning on my Fall board!

    1. Thanks Marcie, it was fun trying to come up with a recipe that emulates fall. I hope you like it, thanks for the pin love! 🙂

    1. Thanks Ashley! They were delicious and I loved the change in texture the apples gave the muffin. 🙂

  16. Avatar photo
    Zainab @ Blahnik Baker

    You won me over with these muffins!! I love fall and all it’s great recipes. These muffins include my two favorite fall ingredients!! Can’t wait to try them. Pinned!

    1. haha.. hurray! 🙂 They use my favorite 2 fall ingredients too, sounds like we on the same wavelength. Thanks for pinning Zainab, hope you like it!

  17. Looks so good- I know my kids will love these for breakfast. AND….. your images are beautiful my friend. LOVE!!!!!

    1. It was always my favorite when my mom gave us muffins for breakfast, and still is. hehe. 🙂 I hope your kiddos like them Gina. Thanks so much on the photography encouragement, I have some awesome photography friends {ahem… you!} to help show me what to do. 🙂

  18. Avatar photo
    Jennifer Onvie

    These look great! I’ve made apple muffins and pumpkin muffins but never the two together, good idea. 🙂

    1. Don’t you love it when two good muffins can come together in harmony! 🙂 These are awesome, I hope you get a chance to try them Jennifer!

  19. I want to pick the pecans off the top of all those delicious look’n muffins! These would be great to have around for in the morning when we’re rushing out the door!

    Oh, my fall food thought would be….pumpkin, acorn squash and apples.

    1. Oh… acorn squash. Definitely one of my favorites, yum! Yes, these were definitely a great grab and go breakafast, especially for the hubbie. Thanks for stopping by Tahny and congrats on the blogversary!