Apple Pumpkin Muffins

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Apple Pumpkin Muffins topped with pecans in a wooden box

A great fall recipe that combines all of your favorite fall flavors. These Apple Pumpkin Muffins are 100% whole wheat and are a great healthy grab and go breakfast.

I don’t know if you’ve noticed but we are officially in full swing of the fall season.  Pinterest is blowing up with pumpkin recipes and the stores have fall {and Christmas} decorations out.  With the feeling and smell of fall in the air myself and a couple of other awesome bloggers joined together to bring you some of the best fall recipes out there!

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What food comes to mind when you think Fall?  I tend to think of Pumpkin recipes, Apple Pie, Caramel Apples, Roasted Turkey, Pecan Pie, Sweet Potatoes, and cranberries.  Well, for this Fall Recipe roundup I thought I would combine a few of those favorites into one delicious healthy muffin.  No, I didn’t make one the weird muffins you would see on Cupcake Wars; like turkey, cranberry, mashed potato muffin. I made a sweet but healthy Apple Pumpkin Muffin topped with Pecans.  This muffin is also 100% whole wheat and uses no oil, milk, or butter! 🙂 It is absolutely delicious and totally reminds me of everything Fall. The one problem I did have while making it was, for some reason the cupcake liners were sticking to the muffin. So if anyone has recommendations on how to solve that problem. PLEASE let me know! Other than that, these are a winner!

To get started, preheat oven to 350º.  Core and peel 1 small granny smith apple. Dice into small pieces, you should have about 1/2 cup. Set aside.

Apple Pumpkin Muffin 4

In a large bowl, mix 1 1/2 cup of King Arthur whole wheat flour, 1/2 cup of brown sugar, 1 1/4 teaspoon of pumpkin pie spice, 3/4 teaspoon of baking powder, 1/2 teaspoon of baking soda, and 1/2 teaspoon of salt. Mix till combined.

Apple Pumpkin Muffin 1

Next, add 3/4 cup of pumpkin puree.

Apple Pumpkin Muffin 2

As well as 1/2 cup of unsweetened apple sauce, 1/2 cup of vanilla greek yogurt, and 2 eggs.

Apple Pumpkin Muffin 3

Using a handheld electric mixer, mix until wet and dry ingredients are combined.

Apple Pumpkin Muffin 5

Stir in 1/2 cup of diced granny smith apples.

Apple Pumpkin Muffin 6

Put cupcake liners in muffin tins and fill each liner all the way with apple pumpkin mixture. Top with chopped pecans. {optional}

Apple Pumpkin Muffin 8

Bake for 22-24 minutes. Until toothpick comes out clean when inserted into muffin.

Apple Pumpkin Muffin 9

Remove from oven and let sit for 5-10 minutes.

Apple Pumpkin Muffin 10

Serve for a grab and go break for a quick afternoon snack.

Apple Pumpkin Muffin 12

Apple Pumpkin Muffin 10

Apple Pumpkin Muffins

  • Author: Krista
  • prep_time Prep Time: 10 mins
  • cook_time Cook Time: 24 mins
  • total_time Total Time: 34 mins
  • yield Yield: 12 -14 muffins 1x
  • category Category: Breakfast, Bread & Dough



  • 1/2 cup of diced granny smith apple {cored & peeled}, about 1 apple
  • 1 1/2 cup of King Arthur Whole Wheat Flour
  • 1/2 cup brown sugar
  • 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
  • 1/2 cup of apple sauce {unsweetened}
  • 1/2 cup vanilla greek yogurt
  • 2 eggs
  • chopped pecans for topping {optional}


  1. Preheat oven to 350 degrees
  2. In a large bowl, mix King Arthur whole wheat flour, brown sugar, pumpkin pie spice, baking powder, baking soda, and salt. Mix until combined.
  3. Next, add pumpkin puree, unsweetened apple sauce, vanilla greek yogurt, and eggs.
  4. Using a handheld electric mixer, mix until wet and dry ingredients are combined.
  5. Stir in diced granny smith apples.
  6. Put cupcake liners in muffin tins and fill each liner all the way with apple pumpkin mixture. Top with chopped pecans. {optional}
  7. Bake for 22-24 minutes. Until toothpick comes out clean when inserted into muffin.
  8. Remove from oven and let sit for 5-10 minutes.


Recipe inspired by [The Comfort of Cooking|]


 Kleinworth & Co.,Recipe Round-Up, recipe sharing, monthly recipe sharing blog round-up, blog party

Apple Cake with Brown Sugar Glaze from Let’s Dish

Chocolate Peanut Butter Caramel Pretzel Poppers from Reasons to Skip the Housework

Apple Ginger Coctail from One Martini at a Time

Caramelized Pear Turnovers from Kleinworth & Co.

Apple Fritters from In the Moment With

Rosh Hashanah Apple Cake from Random-osity

Apple Pumpkin Muffins from Joyful Healthy Eats

Chocolate Pecan Pie Granola from Little by Little

Crock Pot Tuscan Bean Soup from Mostly-Homemade Mom

Apple Cupcakes with Salted Caramel Frosting from Nap-Time Creations

Do you want to participate in future Recipe Round-Up’s & join in on the fun??

email Gina at Kleinworth & Co (chichomeschoolmama{at}att{dot}net) for details.


Hey There

Hi! I'm the recipe developer and food photographer behind all these easy healthy recipes! I love food, Jesus, morning lattes, and am obsessed with fantasy football! { more }

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54 Responses
  1. Anne

    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. Krista

      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. Alena

    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. Krista

      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. Andra

    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. Krista

      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. Erin

    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. Krista

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

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