Apple Pecan Muffin

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I love the aroma of apples baking in the oven! What a delicious, warm aroma that fills your home. As such, experimenting with different apple recipes is so much fun! This led to a new recipe Apple Pecan Muffin that combines elements from an Apple Pie and a spiced muffin! Plus it includes a wonderful twist by using Almond Flour adding a nutty undertone. My recipe tends to go heavy on a variety of spices but of course you can adjust to your own preference! Isn’t that the fun part of a recipe – the chance to make it your own!  

Apple Pecan Muffin with Whipped Cream
Apple Pecan Muffins

Apple Muffin Recipe

There are basically four steps to making the Apple Pecan Muffins. We start with the Apple Pie filling, then the Pecan topping, followed by the batter and then baking the muffins. Make the Apple Pie Filling first and placed in the refrigerator to cool while making the muffins. (Consider making the filling ahead of time storing in the refrigerator.)   The Pecan Topping is quick to assemble and can be made while the Apple Pie filling is cooking on the stovetop.

The Muffin ingredients list looks long but it is mainly the different spices and this is where you need to decide the level of spices to add. I like to experiment with different ingredients that include Coconut Flour and Coconut Sugar. If you do not have Coconut Flour then just substitute Almond Flour. If you wish to use white sugar instead of Coconut Sugar it is a 1 to 1 substitution. When making the Apple Pecan Muffins batter, try to use Buttermilk because a substitute will not fully replace the flavor. But when in a pinch, you can mix together Milk and Vinegar as a substitution for Buttermilk. Just be sure to let the Milk mixed with Vinegar rest for five minutes to ensure the milk has thickened and curdled slightly.

Apple Pecan Muffins in a Basket
Apple Pecan Muffins in a Basket

Baking the Apple Muffins

Now that we made the batter it is time to bake the muffins! Line a 12 cup muffin pan adding about ¼ cup batter to each cup. Make a small well into each muffin cup adding about 1 tablespoon of the Apple Pie Filling. Top with the Pecan Topping and bake! The Apple Pie Filling makes about two dozen of the Apple Pie Muffins. Or make one recipe using the remaining Apple Pie filling for another recipe! For more Apple Pie Filling consider using a jumbo muffin tin! When serving consider adding Whipped Cream or Vanilla Ice Cream! It is a heavenly dessert!

Apple Pecan Muffins Served
Apple Pecan Muffins Served!
Apple Pecan Muffin with Whipped Cream

Apple Pecan Muffin

Pin Recipe
Apple Pecan Muffin is a wonderful blend of Apple Pie with a Spiced inspired muffin. It includes a wonderful twist by using Almond Flour adding a nutty undertone. Plus you can add adjust the Spices and Coconut Sugar depending upon the level of spices and sweetness preferred. When baking the muffins, a delicious aroma fills your home! It does not get much better!
5 from 3 votes
Print Pin Rate
Course: Dessert, Muffins
Cuisine: American
Keyword: Apple Pecan Muffin
Prep Time: 25 minutes
Cook Time: 30 minutes
Total Time: 55 minutes
Servings: 12 Muffins
Calories: 299kcal
Author: Bernice


  • Cutting board and knife
  • Medium size saucepan with lid
  • Medium size bowl with lid (or other option to seal)
  • 2 Small bowls
  • Large mixing bowl
  • 12 cup muffin tin
  • Cookie cooling rack


Apple Pie Filling Ingredients

  • 5 Apples medium
  • 2 tbsp Water
  • 3 tbsp Butter melted
  • 1 to 2 tsp Cinnamon
  • 1/4 to 1/3 cup Coconut Sugar

Pecan Topping Ingredients

  • 1/4 cup Almond Flour
  • 1 tsp Coconut Flour
  • 3/4 tsp Cinnamon
  • 1 tbsp Coconut Oil melted
  • 1 tbsp Maple Syrup
  • 1/3 cup Pecans chopped

Muffin Dry Ingredients

  • 2 cups Almond Flour
  • ¼ cup Coconut Flour
  • 1/2 cup Coconut Sugar
  • 1/2 tsp Salt
  • 1/2 tsp Baking Soda
  • 1 1/2 tsp Baking Powder
  • 1 tsp Cinnamon
  • ¼ tsp Nutmeg
  • ¼ tsp Cloves
  • ¼ tsp Ginger

Muffin Wet Ingredients

  • 1 tsp Vanilla
  • 1 cup Buttermilk or 2% Milk + 1 tsp Vinegar
  • 3 tbsp Butter melted
  • 2 Eggs lightly beaten


  • Whipped Cream


Oven Preparation

  • Preheat oven to 375 degrees.
  • Line or spray a 12 cup muffin tin.
  • Muffins bake for 25 to 30 minutes.

Apple Pie Filling Preparation

  • Peel, core and dice apples depending upon how large or small you prefer. 
  • Melt the butter in a medium size saucepan.
  • Stir in apples. Add cinnamon to coat the apples.
  • Stir in the coconut sugar and water. 
  • Cover and cook stirring occasionally for about 10 minutes or until tender.
  • Place in a medium size bow, cover and place in the refrigerator to slightly cool. 

Pecan Toppings Preparation

  • In a small bowl, mix together all ingredients except pecans.
  • Fold the chopped pecans into the mixture.

Muffin Preparation

  • In a large bowl, mix together the dry ingredients.
  • If using Milk and Vinegar as a substitution for Buttermilk, stir together the Milk and Vinegar letting it sit for five minutes. 
  •  In a smaller bowl, mix together the wet ingredients.
  • Blend the wet ingredients into the dry ingredients
  • Line a 12 cup muffin tin, add a little less than 1/4 cup batter to each cup.
  • Make a small well in each muffin batter.
  • Take the apple pie filling out of the refrigerator.
  • Add about 1 tablespoon of the apple pie filling into the well.  
  • Top with the Pecan topping.
  • Bake for 25 to 30 minutes until brown on top.

Recipe Notes

Calories do not include the whipped cream or any other topping that could be used such as ice cream.
Nutrition Facts
Apple Pecan Muffin
Amount Per Serving (12 g)
Calories 299 Calories from Fat 180
% Daily Value*
Fat 20g31%
Saturated Fat 6g38%
Cholesterol 44mg15%
Sodium 240mg10%
Potassium 196mg6%
Carbohydrates 25g8%
Fiber 5g21%
Sugar 15g17%
Protein 6g12%
Vitamin A 280IU6%
Vitamin C 3.5mg4%
Calcium 113mg11%
Iron 1.2mg7%
* Percent Daily Values are based on a 2000 calorie diet.

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