Whole Wheat Apple Pecan Muffins

Whole Wheat Apple Pecan & Cinnamon Crumble Muffins

Oh Sunday, how I love you so. Waking up to nothing more than the sunlight, having all the time in the world to sip on my morning coffee, hitting a great workout with my love, and time for recipes. I couldn't think of a better day if I tried.

The end of August is quickly approaching, and here in NE Ohio, it's actually starting to feel like it. Our average high's have been in the seventies with zero humidity, very chilly nights, and of course pre season and HS football. Fall is my absolute favorite time of the year; my birthday and anniversary fall in October, cooler weather and football begins in early September, and pumpkin, apple, cinnamon spice everything. I love the taste, smell, and look of anything that has to do with autumn, if I could live in these short few months for forever, I really think I would.

Although I do love pumpkin spice season more than another time of the year, I also love waiting for the perfect moment to break out the pumpkin candles and cookies. I talked myself in circles this weekend over whether or not I should just go for it and make a pumpkin recipe, or try to hold off for another few weeks. Well, I talked myself down and was equally excited when I decided on these Apple Pecan Muffins. It's so easy to forget about this classic duo with all of the hype around pumpkin, but apple and cinnamon has to be hands down one of my favorite combinations in the fall. Sometimes I even cook down apples on the stove with a ton of cinnamon to satisfy a sweet tooth during the week. I just love it that much.

These healthy whole wheat muffins mimic bakery muffins to the crumb. I'm not kidding, they might just be the best muffins I have ever made. They are moist, fluffy, tall and flavorful. Unlike some apple muffins, these actually taste like apple, not just cinnamon with chunks of apples here and there. They are completely refined sugar free and only require a half cup of maple syrup and a few tablespoons of coconut sugar, which both can be omitted if necessary. The whole wheat flour adds a bit of fiber and nutrients to the muffins, also giving them a rich amber color and wholesome taste. I hope you give these a try, I promise you will love them as much as we do!

Apple Pecan & Cinnamon Crumble Muffins

What You Will Need

(Dry) Muffin Ingredients: 

  • 2 cups whole wheat flour

  • 2 tsp. baking soda

  • 2 tsp. cinnamon

  • 1 tsp. nutmeg

  • 1/2 tsp. salt

  • 2 tbsp. coconut sugar, or brown sugar

  • 1/2 cup chopped pecans

(Wet) Muffin Ingredients:

  • 2 cups grated apples, or very finely chopped - *I used a sweeter apple such as fuji or gala to naturally accompany the tart greek yogurt

  • 2 eggs

  • 1/2 cup maple syrup, or honey

  • 1/3 cup whole fat greek yogurt

  • 1/2 cup unsweetened applesauce

  • 2 tsp. vanilla extract

Crumb Topping Ingredients:

  • 2 tbsp. whole wheat flour

  • 1 tsp. cinnamon

  • handful of chopped pecans

  • 1 tbsp. diced, cold butter


Preheat the oven to 425ºF and grease or line a muffin tin. While preheating, prepare the crumb topping by combining flour, cinnamon, chopped pecans and diced butter. You can substitute coconut oil for butter, however you need to melt it and let it completely harden before using. Begin to press the topping ingredients together using a fork or your hands. Small pebble-like balls will start to form, or the crumb topping will hold shape when pressed together. Set aside or in the fridge to begin muffin batter.

In a large mixing bowl, sift together the whole wheat flour, baking soda, cinnamon, nutmeg, and salt. Whole wheat flour does often contain bran, which can make your baked goods more dense. By sifting the flour, you will separate it from the bran, as well as accurately measure the flour. Fold in the chopped pecans and mix well.

Grate or finely chop 2 cups of sweet apples (2-3 apples) and set aside. In a separate mixing bowl, combine eggs, maple syrup, greek yogurt, applesauce, and vanilla extract. Once combined, gently fold in the grated apples until evenly coated. Be sure not to over mix and create air bubbles.

Carefully fill 12 muffin cups, or a greased tin, with the muffin batter. This recipe made 12  medium sized muffins. Generously sprinkle the crumb topping over the wet batter, making sure to coat the muffins evenly.

Place in the oven for 5 minutes at 425ºF, followed by reducing the heat to 350ºF for an additional 15-22 minutes. The surge of heat will cause the muffins to rise quickly, and then cook slowly to retain the moisture and bake evenly throughout. 

Let cool and enjoy! These muffins are the perfect late night treat, or even a great coffee sidekick. I guarantee you won't even know they're actually healthy!

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